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  • Chemistry  (74,703)
  • General Chemistry  (10,869)
  • 1990-1994  (49,875)
  • 1970-1974  (24,828)
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  • 1
    ISSN: 0886-9383
    Keywords: PLS regression algorithm ; Kernel ; Many-variable data sets ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A fast PLS regression algorithm dealing with large data matrices with many variables (K) and fewer objects (N) is presented For such data matrices the classical algorithm is computer-intensive and memory-demanding. Recently, Lindgren et al. (J. Chemometrics, 7, 45-49 (1993)) developed a quick and efficient kernel algorithm for the case with many objects and few variables. The present paper is focused on the opposite case, i.e. many variables and fewer objects. A kernel algorithm is presented based on eigenvectors to the ‘kernel’ matrix XX TYYT, which is a square, non-symmetric matrix of size N × N, where N is the number of objects. Using the kernel matrix and the association matrices XXT (N × N) and YYT (N × N), it is possible to calculate all score and loading vectors and hence conduct a complete PLS regression including diagnostics such as R2. This is done without returning to the original data matrices X and Y. The algorithm is presented in equation form, with proofs of some new properties and as MATLAB code.
    Additional Material: 5 Ill.
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  • 2
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 8 (1994), S. 169-174 
    ISSN: 0886-9383
    Keywords: Kernel algorithm ; PLS ; SVD ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Lindgren et al. (J. Chemometrics, 7, 45-49 (1993)) published a so-called kernel algorithm for PLS regression of Y against X when the number of objects is very large. The algorithm is based solely on deflation of the cross-product matrices XTX, YTY and XTY. The algorithm is now described in a shorter and more transparent way and compared with a similar algorithm for the singular value decomposition of XTY.
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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
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  • 4
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 8 (1994), S. 37-44 
    ISSN: 0886-9383
    Keywords: Bootstrap ; Confidence interval ; Non-linear regression ; Monte Carlo methods ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Non-linear regression models describing the toxicity of a mixture of rotenone and pyrethrins as an insecticide, the catalytic dehydration of n-hexyl alcohol and the Michaelis-Menten model for characterizing reaction rates in enzyme systems will be used to illustrate the accuracy of bootstrap methods in non-linear regression. Classical and bootstrap confidence intervals for the parameter estimates will be presented.
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  • 5
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 8 (1994), S. 97-98 
    ISSN: 0886-9383
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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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
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  • 7
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 8 (1994), S. 147-154 
    ISSN: 0886-9383
    Keywords: RAFA ; GRAM ; Eigenvalue problem ; Complex solution ; Degenerate solution ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Rank annihilation factor analysis (RAFA) is a method for multicomponent calibration using two data matrices simultaneously, one for the unknown and one for the calibration sample. In its most general form, the generalized rank annihilation method (GRAM), an eigenvalue problem has to be solved. In this first paper different formulations of GRAM are compared and a slightly different eigenvalue problem will be derived. The eigenvectors of this specific eigenvalue problem constitute the transformation matrix that rotates the abstract factors from principal component analysis (PCA) into their physical counterparts. This reformulation of GRAM facilitates a comparison with other PCA-based methods for curve resolution and calibration. Furthermore, we will discuss two characteristics common to all formulations of GRAM, i.e. the distinct possibility of a complex and degenerate solution. It will be shown that a complex solution-contrary to degeneracy-should not arise for components present in both samples for model data.
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  • 8
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 8 (1994), S. 179-180 
    ISSN: 0886-9383
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 9
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 8 (1994), S. i 
    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
    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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  • 11
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 8 (1994), S. 245-261 
    ISSN: 0886-9383
    Keywords: Factor analysis ; Spectral resolution ; Two-dimensional luminescence ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A factor analysis algorithm that estimates the spectra of mixture components using the set of most dissimilar rows and/or columns is described and illustrated. This algorithm uses the distance as a measure of spectral similarity and is suitable for application to a variety of the bilinear matrix-formatted data types produced by hyphenated and multidimensional analytical techniqes. The algorithm requires that the data matrix contain at least one row or column that corresponds to the pure spectrum of each component to effect accurate spectral resolution. The performance of the method is illustrated using the resolution of excitation and emission spectra of up to four components from experimental fluorescence excitation-emission matrices (EEMs). In the case of the EEM, characteristic bands in an emission spectrum effect resolution of the excitation spectrum of the corresponding component, while characteristic bands in an excitation spectrum lead to resolution of the corresponding emission spectrum. The use of the set of most dissimilar rows and columns to evaluate the degree of overlap in the component spectra and compare the quality of row and column solutions is also described.
    Additional Material: 6 Ill.
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  • 12
    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: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 14
    ISSN: 0886-9383
    Keywords: Rank annihilation ; Principal components ; Procrustes rotation ; Multivariate analysis ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: It is shown that the DATa ANalysis (DATAN) algorithm can be expressed in terms of rank annihilation factor analysis (RAFA). Subsequent advances in RAFA are applied to DATAN to eliminate the problems and restrictions associated with DATAN. The extension of DATAN in terms of the trilinear decomposition algorithm is discussed.
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  • 15
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 8 (1994), S. 299-301 
    ISSN: 0886-9383
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 16
    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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  • 17
    ISSN: 0886-9383
    Keywords: Resolvability ; Evolutionary factor analysis ; Variable selection ; Window factor analysis ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A method for selecting variables in the non-sequential direction of a two-way data matrix (e.g. wavelength in diode array HPLC) is described. Composition 1 and 2 resolvability indices are calculated according to the size of eigenvalues of uncentred data matrices as a window is moved along the sequential direction. A double-window technique is then performed where resolvability indices are calculated as a window is moved along the non-sequential direction. Some regions have higher resolvability indices and hence are more useful for resolution. Variables are ranked according to resolvability. Two simulations are analysed and it is shown that it is possible to obtain good resolution on a small subset of the original variables.
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  • 18
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 8 (1994), S. i 
    ISSN: 0886-9383
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 19
    ISSN: 0886-9383
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 20
    ISSN: 0887-3585
    Keywords: ribonuclease T1 ; functional cooperativity ; double mutant cycle ; subsite ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We report on the functional cooperativity of the primary site and the sub-site of ribonuclease T1 (RNase T1; EC 3.1.27.3). The kinetic properties of the single Tyr-38-Phe and Asn-98-Ala mutants have been compared with those of the corresponding double mutant. The Tyr-38-Phe mutation has been used to probe enzyme-substrate interactions at the primary site; the Asn-98-Ala mutation monitors subsite interactions.1 In addition to the dinucleoside phosphate substrate GpC, we measured the kinetics for GpMe, a synthetic substrate in which the leaving nucleoside cytosine has been replaced by methanol. All data were combined in a triple mutant box to analyze the interplay between Tyr-38, Asn-98, and the leaving group. The free energy barriers to kcat, introduced by the single Tyr-38-Phe and Asn-98-Ala mutations are not additive in the corresponding double mutant. The energetic coupling between both mutations is independent of the binding of the leaving cytosine at the subsite. We conclude that the coupling of the Tyr-38-Phe and Asn-98-Ala mutations arises through distortion or reorientation of the 3′-guanylic acid moiety bound at the primary site. The experimental data indicate that the enzyme-substrate interactions beyond the scissile phosphodiester bond contribute to catalysis through the formation of new or improved contacts in going from ground state to transition state, which are functionally independent of primary site interactions. © 1994 John Wiley & Sons, Inc.
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  • 21
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    ISSN: 0887-3585
    Keywords: protein structure ; secondary structure ; peptide geometry ; Ramachandran plot ; β-turns ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The polypeptide of a protein molecule can be considered as a chain of Cα atoms linked by pseudobonds between the Cα atoms of successive amino acid residues. This paper presents an analysis of the angle and dihedral angles made by these pseudobonds in protein structures determined at high resolution by X-ray crystallography. This analysis reveals a strong correlation between Cα geometry and the protein fold. The regular features of protein secondary structure such as α-helix and α-sheet are very clearly defined. In addition, it is possible to identify with some confidence the discrete populations of particular conformations of α-turn. Comparison with the traditional Ramachandran type of plot demonstrates that an analysis of protein structure on the basis of Cα geometry provides a richer description of protein conformation. In addition, the characteristics of this geometry could be a useful guide in model building of protein structure. © 1994 John Wiley & Sons, Inc.
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  • 22
    ISSN: 0887-3585
    Keywords: tertiary structure prediction ; reduced protein model ; lattice protein models ; dynamic Monte Carlo simulations ; potentials of mean force ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A new hierarchical method for the simulation of the protein folding process and the de novo prediction of protein three-dimensional structure is proposed. The reduced representation of the protein α-carbon backbone employs lattice discretizations of increasing geometrical resolution and a single ball representation of side chain rotamers. In particular, coarser and finer lattice backbone descriptions are used. The coarser (finer) lattice represents Cα traces of native proteins with an accuracy of 1.0 (0.7) Å rms. Folding is simulated by means of very fast Monte Carlo lattice dynamics. The potential of mean force, predominantly of statistical origin, contains several novel terms that facilitate the cooperative assembly of secondary structure elements and the cooperative packing of the side chains. Particular contributions to the interaction scheme are discussed in detail. In the accompanying paper (Kolinski, A., Skolnick, J. Monte Carlo simulation of protein folding. II. Application to protein A, ROP, and crambin. Proteins 18:353-366, 1994), the method is applied to three small globular proteins. © 1994 John Wiley & Sons, Inc.
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  • 23
    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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  • 24
    ISSN: 0887-3585
    Keywords: staphylococcal nuclease ; nonproductive substrate binding to ; subsites of ; active site mutants of ; oligonucleotide binding to ; Ca2+ binding to ; Mn2+ binding to ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: By a combination of NMR docking and model building, the substrate binding site on staphylococcal nuclease was found to accommodate a trinucleotide and to consist of three subsites, each interacting with a single nucleotidyl unit of DNA. Binding of the essential Ca2+ activator and substrate cleavage occur between subsites 1 and 2. Hence, catalytically productive binding would span subsites 1 and 2 while nonproductive binding would span subsites 2 and 3. Lys-49 is near subsite 1, and Lys-84 and Tyr-115 interact with substrates at sub site 3 [Weber, D. J., Gittis, A. G., Mullen, G. P., Abeygunawardana, C., Lattman, E. E., Mildvan, A. S. Proteins 13:275-287, 1992]. The proposed locations of these subsites were independently tested by the effects of the K49A, K84A, and Y115A mutations of staphylococcal nuclease on the binding of Mn2+, Ca2+, and the dinucleotide and trinucleotide substrates, 5′-pdTdA, dTdA, and dTdAdG. These three mutants have previously been shown to be fully active and to have CD and 2D NMR spectra very similar to those of the wild-type enzyme (Chuang, W.-J., Weber, D. J., Gittis, A. G., Mildvan, A. S. Proteins 17:36-48, 1993). All three mutant enzymes and their pdTdA and dTdA complexes (but not their dTdAdG complex) bind Mn2+ and Ca2+ more weakly than the wild-type enzyme by factors ranging from 2 to 11. The presence of a terminal phosphate as in 5′-pdTdA raises the affinity of the substrate for staphylococcal nuclease and its three mutants by two orders of magnitude and for the corresponding enzyme-metal complexes by three to four orders of magnitude, suggesting that the terminal phosphate is coordinated by the enzyme-bound divalent cation. Such complexation would result in the nonproductive binding of 5′-pdTdA at subsites 2 and 3. Accordingly, the K84A and Y115A mutations significantly weaken the binding of 5′-pdTdA and its metal to staphylococcal nuclease by factors of 2.2 to 37.8, while the K49A mutation has much smaller or no effect. Such nonproductive binding explains the low activity of staphylococcal nuclease with small substrates, especially those With a terminal phosphate. Similarly, the K84A and Y115A mutations weaken the binding of dTdA and its metal complexes to the enzyme by factors of 3.4 to 13.1 while the K49A mutation has smaller effects indicating significant nonproductive binding of dTdA. The trinucleotide dTdAdG binds more tightly to wild-type and mutant staphylococcal nuclease and to its metal complexes than does the dinucleotide dTdA by factors of 2.4 to 12.2, reflecting the occupancy of an additional subsite. Predominantly productive binding of dTdAdG is indicated by the 1.7- to 8.3-fold lower affinities of the K49A, K84A, and Y115A mutants for the trinucleotide and its metal complexes. The largest effects on dTdAdG binding are seen with the Y115A mutation presumably reflecting the dual role of Tyr-115 both in donating a hydrogen bond to a phosphodiester oxygen between subsites 2 and 3 and in stacking onto the guanine base at subsite 3. © 1994 John Wiley & Sons, Inc.
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  • 25
    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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  • 26
    ISSN: 0887-3585
    Keywords: serine carboxypeptidase ; protein modeling ; mutation analysis ; comparative modeling ; cathepsin A ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The deficiency of the lysosomal protective protein/carboxypeptidase L (CARB L) causes the lysosomal storage disorder, galactosialidosis, characterized by neuraminidase and β-galactosidase deficiencies in patients' cells. The three enzymes form a complex inside the lysosome, and the neuraminidase and β-galactosidase deficiencies are secondary to CARB L deficiency. Sequence similarity and common enzymological properties suggest that the protomeric tertiary structure of CARB L is conserved within a family of serine carboxypeptidases which includes the yeast carboxypeptidase Y, killer expression I gene product and several plant carboxypeptidases. We used this homology to build a model of the CARB L structure based on the recently published X-ray atomic coordinates of the wheat carboxypeptidase II (CPDW-II) which shares 32% primary structure identity with CARB L. Small insertions and deletions were accommodated into the model structure by energy minimization using the DREIDING II force field. The Cα atomic-coordinates of the final CARB L model have a RMS shift of 1.01 Å compared to the corresponding conserved residues in the CPDW-II template structure. The correct orientation of the homologous catalytic triad residues Ser150, His429 and Asp392, the potential energy calculations and the distribution of hydrophobic and hydrophillic residues in the structure all support the validity of the CARB L model. Most missense mutations identified in galactosialidosis patients were located in secondary structural elements except for the Tyr211→Asn mutation which is in a loop. The other mutant residues have their side chains deeply buried in the central β-sheet of the model structure except for the Phe412→Val mutation which is located in the dimer interface. The predicted effects of specific mutations on CARB L structural stability correlates well with recently published transient expression studies of mutant CARB L (Shimmoto, M. et al., J. Clin. Invest., 91:2393-2399, 1993). © 1994 John Wiley & Sons, Inc.
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  • 27
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    ISSN: 0887-3585
    Keywords: electrostatics ; protein conformation ; DelPhi ; hydrophobicity ; RNase H ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: In this paper we discuss the problem of including solvation free energies in evaluating the relative stabilities of loops in proteins. A conformational search based on a gas-phase potential function is used to generate a large number of trial conformations. As has been found previously, the energy minimization step in this process tends to pack charged and polar side chains against the protein surface, resulting in conformations which are unstable in the aqueous phase. Various solvation models can easily identify such structures. In order to provide a more severe test of solvation models, gas phase conformations were generated in which side chains were kept extended so as to maximize their interaction with the solvent. The free energies of these conformations were compared to that calculated for the crystal structure in three loops of the protein E. coli RNase H, with lengths of 7, 8, and 9 residues. Free energies were evaluated with a finite difference Poisson-Boltzmann (FDPB) calculation for electrostatics and a surface area-based term for nonpolar contributions. These were added to a gas-phase potential function. A free energy function based on atomic solvation parameters was also tested. Both functions were quite successful in selecting, based on a free energy criterion, conformations quite close to the crystal structure for two of the three loops. For one loop, which is involved in crystal contacts, conformations that are quite different from the crystal structure were also selected. A method to avoid precision problems associated with using the FDPB method to evaluate conformational free energies in proteins is described. © 1994 John Wiley & Sons, Inc.
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  • 28
    ISSN: 0887-3585
    Keywords: protein crystallography ; four helix bundle ; iron ; macromolecular assembly ; regulation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Ferritin is a 24 subunit protein that controls biomineralization of iron in animals, bacteria, and plants. Rates of mineralization vary among members of the ferritin family, particularly between L and H type subunits of animal ferritins which are differentially expressed in various cell types. To examine ferritin from a highly differentiated cell type and to clarify the relationship between ferritin structure and function, bullfrog red cell L ferritin has been cloned, overexpressed in E. coli, and crystallized under two conditions. Crystals were obtained at high ionic strength in the presence of MnCl2 at a concentration comparable to that of the protein and in the presence of MgCl2 at a concentration much higher than that of the protein. Under both crystallization conditions, the crystals are tetragonal bipyramids in the space group F432 with unit cell dimensions a=b=c= 182 ± 0.5 Å. Crystals obtained in the presence of manganese and ammonium sulfate diffract to 1.9 Å, while those obtained in the presence of magnesium and sodium tartrate diffract to 1.6 Å. Isomorphous crystals have been obtained under similar conditions for a site-directed mutant with a reduced mineralization rate in which Glu-57, -58, -59, and -61 are all replaced by Ala. The structure of wild type L-subunit with magnesium has been solved by molecular replacement using the calcium salt of human liver H subunit (Lawson et al., Nature (London) 349:541-544, 1991) as the model. The crystallographic R factor for the 6-2.2 Å shell is 0.21. The overall fold of human H and bullfrog L ferritins is similar with an rms difference in backbone atomic positions of 0.97 Å. The largest structural differences occur in the D helix and the loop connecting the D and E helices of the four helix bundle. Because red cell L ferritin and liver H ferritin show differences in both rates of mineralization and three-dimensional structure, more detailed comparisons of these structures are likely to shed new light on the relationship between conformation and function. © 1994 John Wiley & Sons, Inc.
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  • 29
    ISSN: 0887-3585
    Keywords: myoglobin ; simulation ; hydration ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: An analysis of a molecular dynamics simulation of metmyoglobin in an explicit solvent environment of 3,128 water molecules has been performed. Both statics and dynamics of the protein-solvent interface are addressed in a comparison with experiment. Three-dimensional density distributions, temperature factors, and occupancy weights are computed for the solvent by using the trajectory coordinates. Analysis of the hydration leads to the localization of more than 500 hydration sites distributed into multiple layers of solvation located between 2.6 and 6.8 Å from the atomic protein surface. After locating the local solvent density maxima or hydration sites we conclude that water molecules of hydration positions and hydration sites are distinct concepts. Both global and detailed properties of the hydration cluster around myoglobin are compared with recent neutron and X-ray data on myoglobin. Questions arising from differences between X-ray and neutron data concerning the locations of the protein-bound water are investigated. Analysis of water site differences found from X-ray and neutron experiments compared with our simulation shows that the simulation gives a way to unify the hydration picture given by the two experiments. © 1994 John Wiley & Sons, Inc.
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  • 30
    ISSN: 0887-3585
    Keywords: myoglobin ; solvation ; dynamics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The dynamics of water at the protein-solvent interface is investigated through the analysis of a molecular dynamics simulation of metmyoglobin in explicit aqueous environment. Distribution implied dynamics, harmonic and quasiharmonic, are compared with the simulated macroscopic dynamics. The distinction between distinguishable solvent molecules and hydration sites developed in the previous paper is used. The simulated hydration region within 7 Å from the protein surface is analyzed using a set of 551 hydration sites characterized by occupancy weights and temperature B-factors determined from the simulation trajectory. The precision of the isotropic harmonic and anisotropic harmonic models for the description of proximal solvent fluctuations is examined. Residence times and dipole reorientation times of water around the protein surface are compared with NMR and ESR results. A correlation between diffraction experiment quantities such as the occupancy weights and temperature factors and the residence and correlation times resulting from magnetic resonance experiments is found via comparison with simulation. © 1994 John Wiley & Sons, Inc.
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  • 31
    ISSN: 0887-3585
    Keywords: carboxypeptidas ; molecular dynamics ; enzymatic mechanisms ; peptidase mechanism ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: An MD simulation of the system carboxypeptidase A (CPA) with the tetrapeptide Val-Leu-Phe-Phe has been performed in order to learn about the substrate disposition just prior to nucleophilic attack. We have explored the model in which the substrate does not substitute the zinc-coordinated water (the “water” mechanism). The simulations do suggest as feasible that the Zn-OH2 group performs a nucleophilic attack on the Phe-Phe peptidic bond. We have also investigated the model in which the carbonyl oxygen displaces the zinc-coordinated water. In this case the substrate and Glu-270 orient themselves to allow an anhydride intermediate during the peptidic bond cleavage (the “anhydride” mechanism). Based on the results of the simulations, both “water” and “anhydride” mechanisms are structurally feasible, although the former model seems more probable on chemical grounds. © 1994 John Wiley & Sons, Inc.
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  • 32
    ISSN: 0887-3585
    Keywords: computer modeling ; protein structure prediction ; α-carbons ; structure evaluation ; molecular dynamics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Generation of full protein coordinates from limited information, e.g., the Cα coordinates, is an important step in protein homology modeling and structure determination, and molecular dynamics (MD) simulations may prove to be important in this task. We describe a new method, in which the protein backbone is built quickly in a rather crude way and then refined by minimization techniques. Subsequently, the side chains are positioned using extensive MD calculations. The method is tested on two proteins, and results compared to proteins constructed using two other MD-based methods. In the first method, we supplemented an existing backbone building method with a new procedure to add side chains. The second one largely consists of available methodology. The constructed proteins are compared to the corresponding X-ray structures, which became available during this study, and they are in good agreement (backbone RMS values of 0.5-0.7 Å, and all-atom RMS values of 1.5-1.9 Å). This comparative study indicates that extensive MD simulations are able, to some extent, to generate details of the native protein structure, and may contribute to the development of a standardized methodology to predict reliably (parts of) protein structures when only partial coordinate data are available. © 1994 John Wiley & Sons, Inc.
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  • 33
    ISSN: 0887-3585
    Keywords: X-ray crystallography ; disulfide oxidoreductases ; FAD ; NADPH ; drug target ; Chagas' disease ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The three-dimensional structure of trypanothione reductase (TR) (EC 1.6.4.8) from Trypanosoma cruzi has been solved at 0.33 nm resolution by molecular replacement using the structure of C. fasciculata TR as a starting model. Elucidation of the T. cruzi TR structure represents the first step in the rational design of a drug against Chagas' disease. The structure of T. cruzi TR is compared with those of C. fasciculata TR as well as human and E. coli glutathione reductase (GR). In the FAD-binding domain, TR has two insertions, each about 10 residues long, which do not occur in GR. The first one is a rigid loop stabilizing the position of helix 91-117 which is responsible for the wider active site of TR as compared to GR. The second insertion does not occur where it is predicted by sequence alignment; rather the residues extend three strands of the 4-stranded β-sheet by one or two residues each. This increases the number of hydrogen bonds within the sheet structure. The structure of the NADPH.TR complex has been solved at 0.33 nm resolution. The nicotinamide ring is sandwiched between the flavin ring and the side chain of Phe-198 which undergoes the same conformational change upon coenzyme binding as Tyr-197 in GR. In addition to Arg-222 and Arg-228, which are conserved in TR and GR, Tyr-221 - the last residue of the second β-sheet strand of the βαβ dinucleotide binding fold - is in hydrogen bonding distance to the 2′ phosphate group of NADPH. © 1994 John Wiley & Sons, Inc.
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  • 34
    ISSN: 0887-3585
    Keywords: catalytic antibody ; chorismate mutase ; crystallization ; X-ray diffraction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The Fab′ fragment of a catalytic antibody with chorismate mutase activity has been crystallized as a complex with the transition-state analog hapten. The complex was crystallized by the vapor diffusion method using ammonium sulfate as the precipitant. The crystals belong to the orthorhombic space group P212121 with unit cell dimensions a = 37.1 Å, b = 63.3 Å, c = 178.5 Å, and there is one Fab' molecule per asymmetric unit. The crystals diffract X-rays to at least 3.0 Å and are suitable for X-ray crystallographic studies. © 1994 John Wiley & Sons, Inc.
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  • 35
    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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  • 36
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    ISSN: 0887-3585
    Keywords: peptide folding ; disulfide framework ; insect toxins ; NMR ; distance geometry ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: An analysis of the sequences of scyllatoxin and charybdotoxin suggested that it would be possible to design a core peptide sequence which would still fold to give the β-hairpin and helix seen in the toxins, but which would eliminate one disulfide and connecting residues. The core sequence was modeled, then synthesized and purified. The cysteines oxidize in air to give the same disulfide pairings as seen in the parent toxins as the major product. The three-dimensional structure of the core sequence peptide, termed Max, was determined using proton NMR spectroscopy and found to be identical in secondary structure to the toxins. However differences were found in the relative orientation of the β-hairpin and helix. The use of this structural motif, found in many insect toxins, as a disulfide framework for exploring sequence/structure/activity relationships is discussed. © 1994 John Wiley & Sons, Inc.
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  • 37
    ISSN: 0887-3585
    Keywords: Fab structures ; viral epitopes ; foot-and-mouth disease virus ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The Fab fragment of the neutralizing monoclonal antibody SD6 elicited against foot-and-mouth disease virus (FMDV) C-SBcl and its complex with a peptide, corresponding to the major antigenic site of FMDV (VPl residues 136-150, YTASARGDLAHLTTT), have been crystallized using the hanging drop vapor diffusion techniques. For the isolated Fab, crystals diffracting to 2.5 Å resolution were obtained at room temperature using ammonium sulfate as precipitant. These crystals are monoclinic, space group C2, and unit cell parameters a = 109.53 Å, b = 89.12 Å, c = 64.04 Å, and β = 112.9° and contain one Fab molecule per asymmetric unit. Crystals from the complex diffract, at least, to 2.8 Å resolution and were obtained, at room temperature, using PEG as precipitant. These crystals are monoclinic, space group P2, and unit cell parameters a = 56.11 Å, b = 60.67 Å, c = 143.45 Å, and β = 95.4°, Density packing considerations indicate that there are two Fab molecules in the asymmetric unit. © 1994 John Wiley & Sons, Inc.
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  • 38
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    ISSN: 0887-3585
    Keywords: microcalorimetry ; heat capacity ; enthalpy ; hydrogen bonding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The energetics of ubiquitin unfolding have been studied using differential scanning microcalorimetry. For the first time it has been shown directly that the enthalpy of protein unfolding is a nonlinear function of temperature. Thermodynamic parameters of ubiquitin unfolding were correlated with the structure of the protein. The enthalpy of hydrogen bonding in ubiquitin was calculated and compared to that obtained for other proteins. It appears that the energy of hydrogen bonding correlates with the average length of the hydrogen bond in a given protein structure. © 1994 John Wiley & Sons, Inc.
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  • 39
    ISSN: 0887-3585
    Keywords: nonlinear elliptic equations ; nonlinear multigrid ; inexact Newton methods ; damped Newton methods ; crambin ; BPTI ; HyHEL-5 ; superoxide dismutase ; rhinovirus ; tryptophan synthase ; electrostatic steering ; Brownian dynamics ; antibody-antigen complex ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The nonlinear Poisson-Boltzmann equation (NPBE) provides a continuum description of the electrostatic field in an ionic medium around a macromolecule. Here, a novel approach to the solution of the full NPBE is developed. This robust and efficient algorithm combines multilevel techniques with a damped inexact Newton's method. The CPU time required for solution of the full NPBE, which is less than that for standard single-grid approaches in solving the corresponding linearized equation, is proportional to the number of unknowns enabling applications to very large macromolecular systems. Convergence of the method is demonstrated for a variety of protein systems. Comparison of the solutions to the linearized Poisson-Boltzmann equation shows that the damping of the electrostatic field around the charge is increased and that the potential scales logarithmically with charge. The inclusion of the full nonlinearity thus reduces the impact of highly charged residues on protein surfaces and provides a more realistic representation of electrostatic effects. This is demonstrated through calculation of potential around the active site regions of the 1,266-residue tryptophan synthase dimer and in the computation of rate constants from Brownian dynamics calculations in the superoxide dismutase-superoxide and antibody-antigen systems. © 1994 John Wiley & Sons, Inc.
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  • 40
    ISSN: 0887-3585
    Keywords: molecular dynamics ; protein simulation ; Cu, Zn superoxide dismutase ; electrostatic loop ; mutants ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Molecular dynamics (MD) calculations have been performed on mutants of superoxide dismutase (SOD) on some residues present in the electrostatic loop. These calculations have provided the solution structures for the mutants Thr-137 → IIe and Arg; Lys-136 → Ala; Glu-132 → Gln; Glu-133 → Gln; Glu-132, Glu-133 → Gln-132, Gln-133 and → Gln-132, Lys-133. The structural and dynamic properties of these mutants have been correlated with the catalytic properties and available spectroscopic data. The water molecule present in the active site close to the copper ion in wild type (WT) SOD is missing in the MD average structure of the Thr-137 → IIe mutant, while this molecule is present in the MD average structures of all the other mutants and of WT SOD. This agrees with the experimental data. This is an important result that shows the validity of our calculations and their ability to reproduce even subtle structural features. Addition of one or more positive charges on the 132 and/or 133 positions does not sizably perturb the structure of the active site channel, while the introduction of a positively charged residue (Arg) on position 137 has a large effect on the structure of the electrostatic loop. Analysis of the MD average structures of these mutants has pointed out that the simple electrostatic effects of charged residues in the channel are not the only factor relevant for enzymatic behavior but that the structure of the electrostatic loop and the location of the charged residues also contribute to the catalytic properties of SOD. © 1994 John Wiley & Sons, Inc.
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  • 41
    ISSN: 0887-3585
    Keywords: protein secondary structure prediction ; pleckstrin homology domain ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A consensus prediction for the secondary structure of the pleckstrin homology (PH) domain is presented. The prediction is based on an analysis of patterns of conservation and variation of homologous protein sequences. The structure is predicted to be formed largely from beta strands with a single alpha helix. © 1994 Wiley-Liss, Inc.
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  • 42
    ISSN: 0887-3585
    Keywords: phospholipase A2 ; n-dodecylphosphorylcholine ; complex ; inhibitor ; X-ray crystal analysis ; molecular dynamics simulation ; interaction ; calcium-binding ; catalytic network ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The crystal structure of n-dodecylphosphorylcholine (n-C12PC)-bovine pancreas phospholipase A2 (PLA2) complex provided the following structural.characteristics: (1) the dodecyl chain of n-C12PC was located at the PLA2 N -terminal helical region by hydrophobic interactions, which corresponds to the binding pocket of 2-acyl fatty acid chain (β-chain) of the substrate phospholipid, (2) the region from Lys-53 to Lys-56 creates a cholinereceiving pocket of n-C12PC and (3) the N-termillal group of Ala-1 shifts significantly toward the Tyr-52 OH group by the binding of the n-C12PC inhibitor. Since the accuracy of the X-ray analysis (R = 0.275 at 2.3 Å resolution) was insufficient to establish these important X-ray insights, the complex structure was further investigated through the molecular dynamics (M D) simulation, assuming a system in aqueous solution at 310K. The M D simulation covering 176 ps showed that the structural characteristics observed by X-ray analysis are intrinsic and also stable in the dynamic state. Furthermore, the M D simulation made clear that the PLA2 binding pocket is large enough to permit the conformational fluctuation of the n-C12PC hydrocarbon chain. © 1994 Wiley-Liss, Inc. © 1994 Wiley-Liss, Inc.
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  • 43
    ISSN: 0887-3585
    Keywords: coiled-coils ; keratin ; intermediate filament proteins ; link segments ; heptad phasing ; computer modeling ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Structural discontinuities have previously been identified in four regions of the coiled-coil rod domain structure present in intermediate filament (IF) protein molecules. These include a point at which a phase shift occurs in the heptad periodicity characteristic of the sequence of polar and apolar residues in α-helical coiled-coils, and three links that lack a heptad substructure. We have studied these regions by computer-based molecular modeling and comparative sequence analysis and conclude that the phasing discontinuity can be accommodated without significant distortion of the overall double-helical chain conformation; the L2 link has a similar conformation in all different types of IF molecules, a favorable conformation being one in which the two strands wrap tightly around each other; the L12 links vary in length between different IF types but contain important sequence similarities suggestive of a partial β structure; the L1 links show larger variations in length, a lower degree of similarity, and probably diverse structures. Variations in the overall charges of the different links suggest that ionic interactions may playa significant role in filament assembly. The results also have general significance for other α-fibrous proteins in which either the characteristic heptad phasing undergoes a discontinuity or where a short non-coiled-coil sequence occurs within a coiled-coil rod domain structure. © 1994 Wiley-Liss, Inc.
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  • 44
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    ISSN: 0887-3585
    Keywords: hydrophobicity ; effective backbone interactions ; folding ; avian pancreatic polypeptide ; parathyroid hormone-related protein ; Monte Carlo ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: ABSTRACT A simplified description and a corresponding force field for polypeptides is introduced. Each amino acid residue is reduced to one interaction site, representing the backbone, and one or two side chain sites depending on its size and complexity. Site-site interactions are parameterized after a hydrophobicity criterium. The treatment of backbone sites is in addition designed to reproduce typical polypeptide hydrogen bonding patterns, as well as yielding conformations in accord with the allowed φ and ψ angles through an effective angle potential. There are no explicit charges in the model. The derived energy functions, which are based on thermodynamic data and sterical consideration of allowed backbone conformations, correspond to the introduction of an effective potential. The model is tested on two small proteins, avian pancreatic polypeptide and a parathyroid hormone-related protein, by simulating folding from an initially extended state using Monte Carlo methods. The reduced amino acid description is able to satisfactorily reproduce the experimentally determined native structures. © 1994 John Wiley & Sons, Inc.
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  • 45
    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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  • 46
    ISSN: 0887-3585
    Keywords: membrane ; protein ; structure ; prediction ; G-protein coupled receptor ; rhodopsin ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Integral membrane proteins (of the α-helical class) are of central importance in a wide variety of vital cellular functions. Despite considerable effort on methods to predict the location of the helices, little attention has been directed toward developing an automatic method to pack the helices together. In principle, the prediction of membrane proteins should be easier than the prediction of globular proteins: there is only one type of secondary structure and all helices pack with a common alignment across the membrane. This allows all possible structures to be represented on a simple lattice and exhaustively enumerated. Prediction success lies not in generating many possible folds but in recognizing which corresponds to the native. Our evaluation of each fold is based on how well the exposed surface predicted from a multiple sequence alignment fits its allocated position. Just as exposure to solvent in globular proteins can be predicted from sequence variation, so exposure to lipid can be recognized by variable-hydrophobic (variphobic) positions. Application to both bacteriorhodopsin and the eukaryotic rhodopsin/opsin families revealed that the angular size of the lipid-exposed faces must be predicted accurately to allow selection of the correct fold. With the inherent uncertainties in helix prediction and parameter choice, this accuracy could not be guaranteed but the correct fold was typically found in the top six candidates. Our method provides the first completely automatic method that can proceed from a scan of the protein sequence databanks to a predicted three-dimensional structure with no intervention required from the investigator. Within the limited domain of the seven helix bundle proteins, a good chance can be given of selecting the correct structure. However, the limited number of sequences available with a corresponding known structure makes further characterization of the method difficult. © 1994 John Wiley & Sons, Inc.
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  • 47
    ISSN: 0887-3585
    Keywords: triglyceride lipase ; proenzyme ; molecular replacement ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A neutral lipase from the filamentous fungus Rhizopus delemar has been crystallized in both its proenzyme and mature forms. Although the latter crystallizes readily and produces a variety of crystal forms, only one was found to be suitable for X-ray studies. It is monoclinic (C2, a = 92.8 Å, b = 128.9 Å, c = 78.3 Å, β = 135.8) with two molecules in the asymmetric unit related by a noncrystallographic diad. The prolipase crystals are orthorhombic (P212121, with a = 79.8 Å, b = 115.2 Å, c = 73.0 Å) and also contain a pair of molecules in the asymmetric unit. Initial results of molecular replacement calculations using the refined coordinates of the related lipase from Rhizomucor miehei identified the correct orientations and positions of the protein molecules in the unit cells of crystals of both proenzyme and the mature form. © 1994 John Wiley & Sons, Inc.
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  • 48
    ISSN: 0887-624X
    Keywords: aromatic polyformals ; 2,2-bis(4-hydroxyphenyl)-1,1,1,3,3,3-hexafluoropropane ; 2,2-bis(4-hydroxyphenyl)propane ; dichloromethane ; polycondensation ; copolycondensation ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A series of fluorine-containing aromatic homopolyformal and copolyformals with a wide range of unit ratio were synthesized by the solution polycondensation of 2,2-bis (4-hydroxyphenyl)-1,1,1,3,3,3-hexafluoropropane (Bisphenol AF) and/or 2,2-bis (4-hydroxyphenyl)propane (Bisphenol A) with dichloromethane, and the effect of the fluorine substitution on the preparation and properties of these polymers was investigated by comparing with those of Bisphenol-A-based homopolyformal without fluorine. Irrespective of the ratio of Bisphenol AF, high-molecular-weight, fluorine-containing polyformals with reduced viscosities of 1.4-5.3 dL/g were obtained in high yields by using dichloromethane as both comonomer and solvent, potassium hydroxide as a base, and N-methyl-2-pyrrolidone as a comedium at 75°C for 4 h. Their solubility increased markedly by the introduction of fluorine atom. Colorless, transparent, and tough films were cast from chloroform solution irrespective of fluorine content. These films had good mechanical properties comparable to that of Bisphenol-A-based homopolyformal. The contact angles by water were larger than 90°, regardless of their fluorine contents, at 25°C. The glass transition temperature and thermal stability increased monotonically with increasing fluorine content. © 1994 John Wiley & Sons, Inc.
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  • 49
    ISSN: 0887-624X
    Keywords: polyurethane ; chromatography ; stoichiometry ; GPC ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The kinetics of formation of polyurethane prepolymers is studied by an analytical technique which involves reactive quenching of the isocyanate, separation of the oligomeric species by GPC, and measurement by UV absorbance of the quenched moieties. The precision of the kinetic parameters and the ratios of the oligomers are determined. The effect of changes in reactant stoichiometry on the ratio of oligomers is measured and compared to the value predicted by an equation from Flory. Toluene diisocyanate is shown to give fewer high oligomers than predicted, while methylene diphenylene diisocyanate gives nearly the predicted values. Tetramethylxylene diisocyanate gives more high oligomers than predicted, an unexpected but possibly important result. Catalyst is shown to increase the reaction rate of the last by more than 200 times. © 1994 John Wiley & Sons, Inc.
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  • 50
    Electronic Resource
    Electronic Resource
    Bognor Regis [u.a.] : Wiley-Blackwell
    ISSN: 0887-624X
    Keywords: polyarylsiloxanes ; -diaminosiloxane ; thermal stability ; percent char ; flame retardance ; hydrolytic stability ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: High molecular weight polymers containing oligosiloxanes in the backbone were made by the reaction of aromatic diols with α,ω-diaminosiloxane homologs. The glass transition temperatures dropped by 30-40°C in a homologous series with each siloxane added. The thermal stability also suffered when increasing the number of siloxane groups. The polymers all displayed high % char measurements and one polymer (disiloxane) tested had a V0 rating by UL-94 testing. The trisiloxane-containing polymer had a high percent elongation at break (〉300%). All the polymers tested were fairly susceptible to hydrolysis. © 1994 John Wiley & Sons, Inc.
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  • 51
    ISSN: 0887-624X
    Keywords: 4-hydroxybenzoic acid ; 6-thioxantone-2-carboxylic acid ; copolyesters ; whiskers ; polycondensation ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: 6-Hydroxythioxanthone-2-carboxylic acid (HTCA) was prepared from commercial dimethylnitroterephthalate via 2-(4'-hydroxythiophenyl) terephthalic acid. HTCA was acetylated and polycondensed in an inert reaction medium at 350 or 400°C. An insoluble and infusible, highly crystalline polyester was obtained, which did not form whisker-like crystals. Furthermore, copolyesters with 4-hydroxybenzoic acid (4-HBA) were synthesized and whiskers were obtained at a molar ratio of 1 : 9 (in favor of 4-HBA). A meltable, nematic copolyester was prepared by cocondensation of silylated 6-acetoxythioxanthone-2-carboxylic acid and silylated 4-acetoxybenzoic acid in bulk. © 1994 John Wiley & Sons, Inc.
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  • 52
    ISSN: 0887-624X
    Keywords: polyimide molecular composite ; crosslinking ; internal acetylene ; laminate processing ; high modulus ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Polyimide/polyimide molecular composite (MC) films comprised of a rigid polyimide derived from biphenyltetracarboxylic dianhydride (BPDA) and p-phenylenediamine (PDA) and a flexible polyimide derived from BPDA and bis (3,3'-diaminodiphenyl) acetylene (intA) and/or oxydianiline (ODA) were prepared by blending the polyamic acid solutions in 7 : 3 weight ratio, and then imidizing the blend films. Acetylene content in the flexible polyimide backbone was controlled by the ratio of intA and ODA. Cold-drawing of the blend polyamic acid films, followed by imidization, gives high modulus polyimide/polyimide MC films. The modulus of the MC films increased almost linearly with the draw ratio, reaching 25.5 GPa for the 40% drawn film. Acetylene groups in the flexible polyimide can be thermally cured to crosslink. The onset of exotherm appeared at 340°C on DSC, reaching maximum at 398°C. After the thermal crosslinking, the MC films maintained the high modulus, though elongation became small. Taking advantage of the crosslinkable acetylene units, two MC films were laminated and processed at 400°C for 20 min under 100 kg/cm2 to give a good-quality laminate film. The interface of the two films was strongly bonded through the crosslinking of acetylene groups. Laminate films maintained the high modulus afforded by the cold-drawing. © 1994 John Wiley & Sons, Inc.
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  • 53
    ISSN: 0887-624X
    Keywords: thermal degradation ; polysiloxane ; alternating copolymer ; thermal isomerization ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 1 Ill.
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  • 54
    ISSN: 0887-624X
    Keywords: 4-methylene-1,3-dioxolane ; nucleophilic compound ; vinyl ether ; ring-opening polymerization ; cationic polymerization ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 2 Ill.
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  • 55
    ISSN: 0887-624X
    Keywords: PMR-15 ; polyimides ; PMR-15 NMR-analyses ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Variations in PMR-15 composites properties could be due to differences in their chemical compositions occurring during the curing cycle. Variations in the composition of the PMR-15 resin were studied for four different curing cycles, to determine the influences of parameters such as the heating rate or the presence of a temperature stage. The resin mixture was sampled at the same four different temperature points in each cycle and analyzed mainly by 1H- and 13C-NMR. Quantitative analysis of the different chemical species were realized by deconvolution of NMR spectra. At a given temperature, the resin contains the same molecules but in proportions which depend on the curing conditions and which reflect differences in the chemical reactivity of the monomeric species. We have precisely defined the temperature ranges at which each of the key reactions (amidization, imidization, exoendo isomerization) occurs. An imine condensation product of NE and MDA has been identified and shown to be present in the resin mixture even at low temperature. As a result of this study, two possible causes of resin alteration during ageing can be put forward: the presence of nonimidized BTDE moieties and the endo-exo isomerization reaction which will result in deformation and, possibly, microcracking, if reticulation of the end-capped nadimides is not total. © 1994 John Wiley & Sons, Inc.
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  • 56
    ISSN: 0887-624X
    Keywords: ammonia/ammonium thiocyanate solvent ; cellulose ; dissolution mechanism ; solid state CP/MAS 13C-NMR ; X-ray ; conformation ; hydrogen bonding ; ammonia mercerization ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Ammonia/ammonium thiocyanate (NH3/NH4SCN) is an excellent swelling agent and solvent for cellulose, even at a high degree of polymerization. Because polymorphic conversion in cellulose has been a long-standing, perplexing, troublesome problem, we have undertaken to study that mechanism. Solid state CP/MAS 13C-NMR and X-ray analysis proved to be very useful analytical techniques for the task. It appears that during temperature cycling, specific cellulosic inter- and intramolecular hydrogen-bonds are broken as polymorphic conversion proceeds sequentially from the polymorph I to III, and finally at total solvation to amorphous. This proceeds correspondingly via transformation of the polymorph conformations of CH2OH from trans-gauche, “tg,” to gauche-trans, “gt,” to gauche-gauche, “gg.” © 1994 John Wiley & Sons, Inc.
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  • 57
    ISSN: 0887-624X
    Keywords: 1,3,4-thiadiazole ; activated difluoride ; aromatic diols ; polyethers ; nucleophilic substitution polymerization ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Seven 1,3,4-thiadiazole-containing polyethers with reduced viscosities of 0.27-1.44 dL/g were synthesized by the high-temperature solution polycondensation of novel activated difluoride, 2,5-bis (4-fluorophenyl)-1,3,4-thiadiazole, with aromatic diols possessing a variety of ring structures. The expected chemical structures were confirmed by IR and 1H-NMR spectroscopy and elemental analysis. Of all the polymers, three polyethers were highly crystalline and soluble only in limited solvents such as concentrated sulfuric acid. The other polyethers were amorphous and dissolved easily in a variety of organic solvents including N-methyl-2-pyrrolidone (NMP), phenols, and chlorinated hydrocarbons. Colorless to slightly yellow-colored, transparent, and tough films could be cast from the NMP solutions of the amorphous polyethers. The mechanical properties of the films were excellent, and their tensile strength, elongation at break, and tensile moduli were in the ranges of 48-72 MPa, 5-7%, and 1.3-1.9 GPa, respectively. The amorphous polyethers had high glass transition temperatures of 204-299°C. All the polyethers were highly thermally and thermooxidatively stable and exhibited no weight loss up to 400°C, with 10% weight loss being recorded at 464-513°C in air. © 1994 John Wiley & Sons, Inc.
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    ISSN: 0887-624X
    Keywords: 1,3-dioxan-2-one ; oxepan-2-one ; copolymer ; characterization ; coordination catalysits ; initiation mechanism ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A new type of copolymer is synthesized in a bulk polymerization from 1,3-dioxan-2-one and oxepan-2-one (∊-caprolactone) using either Sn-oct, ZnAc2, Bu2SnO, or Bu3SnCl as the catalyst. SEC analysis shows that it is possible to achieve high molecular weights and narrow molecular weight distributions. 13C-NMR analysis confirms the existence of copolymers. Conversion studies have been made and reactivity ratios, r1 and r2, have been determined to distinguish between the reactivities of 1,3-dioxan-2-one and oxepan-2-one. The Finemann-Ross method and the Kelen-Tüdös method were used to calculate the ratios and the agreement was good between the methods. The composition of the copolymer agrees with the feed composition at high conversions. Thermal analysis of copolymers by DSC shows crystalline melting resulting from a somewhat blocky copolymer. The glass transition temperatures of the copolymers are in agreement with the Fox equation. The corresponding blends of the two homopolymers show a constant melting point and glass transition temperature. A nonionic insertion mechanism and a Lewis acid alcoholysis mechanism are discussed. © 1994 John Wiley & Sons, Inc.
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    Electronic Resource
    Electronic Resource
    Bognor Regis [u.a.] : Wiley-Blackwell
    ISSN: 0887-624X
    Keywords: liquid crystal polymers ; transesterification ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The stability of a polymeric nematogen's chemical sequence was studied by differential scanning calorimetry, optical microscopy, and 13C-NMR; the nematogen studied was a thermotropic polyester and had a periodic chemical structure. Model compounds were used to investigate transesterfication in the melt at different temperatures with the addition of phenol or benzoic acid as analogues of polymer end groups. Ester interchange reactions at high temperature were found to be partly suppressed when acidic end groups of the periodic nematogen were capped. However, sequence reorganization was completely suppressed in capped nematogens when temperatures remained below the isotropization transition of the nematogen investigated. Rapid disordering of the periodic nematogen was observed above the nematic-isotropic transition, suggesting that both chemical and physical factors play a role in sequence redistribution of periodic nematogens. © 1994 John Wiley & Sons, Inc.
    Additional Material: 8 Ill.
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  • 60
    ISSN: 0887-624X
    Keywords: glycidyl vinyl ether ; carbon dioxide ; (2-oxo-1,3-dioxolan-4-yl) methyl vinyl ether ; cationic polymerization ; poly[(2-oxo-1,3-dioxolan-4-yl) methyl vinyl ether] ; radical copolymerization of OVE ; polymer reaction of P(OVE) ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: (2-Oxo-1,3-dioxolan-4-yl) methyl vinyl ether (OVE) was synthesized with high yield by addition reaction of glycidyl vinyl ether with carbon dioxide using tetrabutylammonium bromide (TBAB) as a catalyst. OVE was also prepared by reaction with β-butyrolactone or sodium hydrogencarbonate in the presence of TBAB as the catalyst. Poly [(2-oxo-1,3-dioxolan-4-yl) methyl vinyl ether] [P(OVE)] was obtained with high yield by cationic polymerization of OVE catalyzed using boron trifluoride diethyl ether complex in dichloromethane. Polymers bearing pendant 5-membered cyclic carbonate groups were also prepared by radical copolymerization of OVE with some electron-accepting monomers. Furthermore, addition reaction of P(OVE) with alkyl amines yielded the corresponding polymer having pendant 2-hydroxyethyl carbamate residue with high conversions. © 1994 John Wiley & Sons, Inc.
    Additional Material: 6 Tab.
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