bluuebunny/crossref_metadata_2025_split huggingface dataset:
A comparative study of various computational approaches in calculating the structure of pyridoxal 5′‐phosphate (PLP)‐dependent β‐lyase protein. The importance of protein environment
Authors: Prabhakar Rajeev , Morokuma Keiji , Musaev Djamaladdin G. 
Published: February 2005

AbstractVarious computational approaches, using molecular mechanics (Amber), semiempirical (AM1), density functional (B3LYP), and various ONIOM methods, have been comparatively investigated for the structure of Escherichia coli NifS CsdB protein. The structure of the entire monomer containing 407 amino acid residues and 579 surrounding water molecules has been optimized. The full geometry optimization in the “active site‐only” approach (including only active site atoms) has been found to give the largest root‐mean‐square (RMS) deviation from the X‐ray structure; a much better agreement has been achieved by keeping the atoms leading to the backbones of some amino acids frozen in their positions in the X‐ray structure. The best agreement has been attained by including the surrounding protein in the calculations using the two‐layer ONIOM (B3LYP:Amber) approach. The results presented in this study conclusively demonstrate the importance of the protein/active‐site interaction on the active‐site structure of the enzyme. The present theoretical study represents the largest system studied at the ONIOM level to date, containing 7992 atoms, including 84 atoms in the QM region and rest in the MM region. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 443–446, 2005
Isolation and characterization of collagen from bigeye snapper (Priacanthus macracanthus) skin
Authors: Jongjareonrak Akkasit , Benjakul Soottawat , Visessanguan Wonnop , Tanaka Munehiko 
Published: February 2005

AbstractAcid‐solubilized collagen (ASC) and pepsin‐solubilized collagen (PSC) were isolated from the skin of bigeye snapper (Priacanthus macracanthus) with yields of 64 and 11 g kg−1 wet weight, respectively. Both ASC and PSC were characterized as type I collagens with no disulfide bonds. Peptide maps of ASC and PSC digested by V8 protease and lysyl endopeptidase showed some differences in peptide patterns and were totally different from those of calf skin collagen. The maximum solubility was observed at pH 4 and 5 for ASC and PSC, respectively. A sharp decrease in solubility of both collagens in acetic acid was found with NaCl concentration above 30 g l−1. Thermal transitions of ASC and PSC in deionized water were observed with Tmax of 30.37 and 30.87 °C, respectively, and were lowered in the presence of acetic acid (0.05 mol kg−1 solution). Therefore, ASC was a major fraction in bigeye snapper skin and it exhibited some different characteristics to PSC. Copyright © 2005 Society of Chemical Industry
Quantification of lycopene in tomato products: comparing the performances of a newly proposed direct photothermal method and high‐performance liquid chromatography
Authors: Bicanic Dane , Fogliano Vincenzo , Luterotti Svjetlana , Swarts Jan , Piani Giovanni , Graziani Giulia 
Published: February 2005

AbstractA new photothermal method suitable for direct, accurate and highly reproducible quantitative measurements of lycopene in tomato products has been introduced. The intrinsic precision of the method is typically better than 0.2%; the repeatability of determination is comparable to that of high‐performance liquid chromatography, with 0.86% least overall error. Copyright © 2005 Society of Chemical Industry
Analyses of tomato peel and seed byproducts and their use as a source of carotenoids
Authors: Knoblich Monika , Anderson Brandi , Latshaw David 
Published: February 2005

AbstractCommercial tomato canning yields two different byproducts. One is the material that results from peeling tomatoes, while the other results from removing the seeds. The peel byproduct contained 100.8 g protein, 256.4 g ash and 299.4 g acid detergent fiber kg−1. Ash content was high because the peel byproduct contained 83.8 g kg−1 sodium as a result of using a sodium hydroxide solution to peel the tomatoes. The seed byproduct contained 202.3 g protein, 51.8 g ash, and 537.9 g acid detergent fiber kg−1. An amino acid analysis of seeds indicated that approximately 60% of the protein results from amino acids. Both byproducts were analyzed for carotenoid content. The lycopene content of peel byproduct was 734 µg g−1 of dry material. Significant amounts of lutein, β‐carotene, and cis‐β‐carotene were also present. Seed byproduct contained 130 µg lycopene kg−1 of dry matter. The content of other carotenoids was approximately half of that present in the peels. Peel and seed byproducts were included at 75 g kg−1 in hen diets to determine the transfer of carotenoids to the yolk. When fed at this concentration, the lycopene content of dry egg yolk was approximately 0.9 µg g−1. Approximately 0.1% of the lycopene in peel byproduct and approximately 0.7% of the lycopene in the seed byproduct was transferred from the feed to the yolk. Lycopene appears more similar to carotene than to oxycarotenoids in its transfer to the yolk. Copyright © 2005 Society of Chemical Industry
The oxidative degradation of the lipid fraction of ripened sausages as influenced by the raw material
Authors: Summo Carmine , Caponio Francesco , Bilancia Maria Teresa 
Published: February 2005

AbstractAn experimental investigation was conducted to assess the actual degree of oxidative degradation of the lipid fraction of 30‐day‐ripened sausages using both commonly used investigations and non‐conventional means, such as the high‐performance size‐exclusion chromatography analysis of polar compounds. Sausages made from pork shoulders from extensive and intensive pig rearing were considered. The obtained results showed a high degree of primary oxidative degradation of the sausage lipid fraction, as evidenced by oxidized triacylglyrerol and peroxide values, while a low secondary oxidation of fats was found, as evidenced by triacylglycerol oligopolymers and 2‐tiobarbituric acid test values. Moreover, the degree of oxidative degradation did not show any significant difference between the two types of sausage, although the samples prepared from extensively reared pigs, as compared with those from intensively reared pigs, showed significantly (p < 0.001) higher contents of polyunsaturated fatty acids and significantly (p < 0.01) lower amounts of saturated fatty acids. Copyright © 2005 Society of Chemical Industry
Influence of ripening stage on volatiles composition, physicochemical indexes and sensory evaluation in two varieties of muskmelon (Cucumis melo L var reticulatus Naud)
Authors: Senesi Emilio , Di Cesare Luigi F , Prinzivalli Caterina , Scalzo Roberto Lo 
Published: February 2005

AbstractThe quality parameters of muskmelon (Cucumis melo L var reticulatus Naud) are often related to sugar content and aroma composition. A study of aroma composition using two different extraction techniques (GC‐HS and GC‐MS extraction concentration) was performed in order to find correlations with sensory descriptors, other quality indices and ripening stage. Two muskmelon varieties (Calypso and Pamir) were assayed at three different ripening stages (unripe, ripe, overripe). Chemical, physical and sensory analyses were performed on the muskmelon samples just after harvest and after 7 days of cold storage. Solid soluble content (SSC) changed from about 10°Bx in unripe samples to about 15°Bx in ripe and overripe samples. Different aroma composition and sensory evaluation were found depending on the ripening stages. The main flavour components detected were esters which increased 10–15‐fold from unripe to ripe and overripe stages. The acceptance judgements by panellists were strongly correlated with the sensory descriptor flavour. High statistical correlations were also found between sensory descriptor flavour and some classes of aroma compounds, mainly with total esters (about 0.66–0.69), formates (0.70) and acetates (0.64 and 0.72). The paper demonstrates that some classes of esters are very important to assess the sensory flavour and overall eating quality of muskmelons. Copyright © 2005 Society of Chemical Industry
Improving the quality of sorghum injera by decortication and compositing with tef
Authors: Yetneberk Senayit , Rooney Lloyd W , Taylor John RN 
Published: February 2005

AbstractInjera is an Ethiopian fermented pancake‐like bread made from cereals, with tef being preferred. Decortication and compositing with tef were evaluated as methods to improve the injera‐making quality of red tannin‐free and tannin‐containing sorghums. Both decortication and compositing improved sorghum injera quality. Concerning decortication, mechanical abrasion was found to be more effective than hand pounding because acceptable injera was obtained with lower milling loss. Good quality injera was produced at an extraction rate of 540 g kg−1 for tannin‐containing and 830 g kg−1 for tannin‐free sorghum. With compositing, good quality injera was produced with a 50:50 (w/w) composite of whole tannin‐containing sorghum and tef. Both processes reduced the tannin content of the flours, which appeared to relieve the inhibiting effects of tannins on the fermentation. Decortication also seemed to improve sorghum flour injera‐making quality by improving flour pasting as a result of reducing the level of interfering substances such as lipids and proteins. In contrast, the improvement brought about by compositing with tef seemed to be due to inherent differences between tef and sorghum starch granules and an increase in the water solubility index of the flour. Compositing seems to be a more useful method of improving sorghum injera quality than decorticating as it avoids the grain loss associated with decortication. Copyright © 2005 Society of Chemical Industry
Water distribution and mobility in herring muscle in relation to lipid content, season, fishing ground and biological parameters
Authors: Jensen Kristina Nedenskov , Jørgensen Bo M , Nielsen Henrik H , Nielsen Jette 
Published: February 2005

AbstractLow‐field 1H nuclear magnetic resonance transverse relaxation profiles were measured on muscle samples from herring differing in catch season (summer or winter), fishing ground (Baltic Sea, North Sea, Skagerrak or Kattegat), biological parameters (maturity status, sex and spawning type), lipid and water content, and catching vessel (the institute's research vessel Dana or commercial fishing vessels). Water mobility and distribution in herring muscle samples were calculated from the NMR signals by the use of multi‐way analysis. The distribution and mobility of water in samples from herring caught by Dana differed according to season, samples from summer herring having two water pools (with T2‐values of 37 and 75 ms) and samples from winter herring having three water pools (with T2‐values of 41, 58 and 102 ms). This difference in number of water pools was also found in samples from herring caught by commercial vessels. It is suggested that samples from herring caught during winter contain an extra pool of inter‐myofibrillar water not present in the samples from herring caught during the summer due to their higher lipid content. The water and lipid content significantly affected the water distribution in both summer and winter herring. The differences in water pools were also reflected in the sensory quality of a marinated herring product. The leaner winter herring corresponding to samples with three water pools were more firm and had less fatty mouth feel than the more fatty summer herring, corresponding to samples with only two water pools. Copyright © 2005 Society of Chemical Industry
Optimization of solid‐phase microextraction methods for GC‐MS determination of terpenes in wine
Authors: Peña Rosa M , Barciela Julia , Herrero Carlos , García‐Martín Sagrario 
Published: February 2005

AbstractSolid‐phase microextraction using a 100 µm poly(dimethylsiloxane) fiber, followed by gas chromatography–mass spectrometry determination, has been optimized for the analysis of some terpenes in wine samples. The best results were obtained by direct immersion of the fiber using a sampling period of 15 min with constant magnetic stirring (1100 rpm) and an extraction temperature of 20 °C. The sample volume was 7 ml with 25% NaCl, in a 15 ml capped vial. Desorption was performed directly in the gas chromatograph injector port over 5 min at 250 °C using the splitless mode. The method is sensitive, with detection limits between 11 and 25 µg l−1, precise, with variation coefficients in the range 1.28–3.71%, and linear over more than one order of magnitude. The related conditions were used for wine sample analyses with recoveries between 71.8 and 90.9%. Solid‐phase microextraction remains an attractive alternative technique due to its rapidity and because it is a solvent‐free extraction. Copyright © 2005 Society of Chemical Industry
Generation and interrogation of a pure nuclear spin state by parahydrogen‐enhanced NMR spectroscopy: a defined initial state for quantum computation
Authors: Blazina D. , Duckett S. B. , Halstead T. K. , Kozak C. M. , Taylor R. J. K. , Anwar M. S. , Jones J. A. , Carteret H. A. 
Published: February 2005

AbstractWe describe a number of studies used to establish that parahydrogen can be used to prepare a two‐spin system in a pure state, which is suitable for implementing NMR quantum computation. States are generated by pulsed and continuous‐wave (CW) UV laser initiation of a chemical reaction between Ru(CO)3(L2) [where L2 = dppe = 1,2‐bis(diphenylphosphino)ethane or L2 = dpae = 1,2‐bis(diphenylarsino)ethane] with pure parahydrogen (generated at 18 K). This process forms Ru(CO)2(dppe)(H)2 and Ru(CO)2(dpae)(H)2 on a sub‐microsecond time‐scale. With the pulsed laser, the spin state of the hydride nuclei in Ru(CO)2(dppe)(H)2 has a purity of 89.8 ± 2.6% (from 12 measurements). To achieve comparable results by cooling would require a temperature of 6.6 mK, which is unmanageable in the liquid state, or an impractical magnetic field of 0.44 MT at room temperature. In the case of CW initiation, reduced state purities are observed due to natural signal relaxation even when a spin‐lock is used to prevent dephasing. When Ru(CO)3(dpae) and pulsed laser excitation are utilized, the corresponding dihydride product spin state purity was determined as 106 ± 4% of the theoretical maximum. In other words, the state prepared using Ru(CO)3(dpae) as the precursor is indistinguishable from a pure state. Copyright © 2004 John Wiley & Sons, Ltd.
The size of the alpha‐effects in methyl transfers correlate with Koopmans' theorem ionization potentials
Authors: Fountain K. R. 
Published: February 2005

AbstractThe size of the alpha‐effects in methyl transfers to the alpha‐nucleophile's peroxide anion and two N‐methylbenzohydroxamate anions correlate strongly with the Koopmans' theorem ionization potentials of the leaving groups. This correlation supports the Shaik and Pross valence bond configuration mixing theory for the SN2 reaction. The Koopmans' theorem ionization potentials of the alpha‐nucleophiles relate to the slopes of the regression plots inversely, indicating that the size of the alpha‐effect depends on a balance between the ability of the alpha‐nucleophile and the leaving group to donate single electron character to the methyl group. Copyright © 2005 John Wiley & Sons, Ltd.
Multiple‐substituent effects on the isomerization of unsymmetrical cis‐1,3‐diphenyltriazenes
Authors: Zhang Huaibin , Barra Mónica 
Published: February 2005

AbstractTrans‐to‐cis photoisomerization of unsymmetrical 4,4′‐disubstituted trans‐1,3‐diphenyltriazenes renders a non‐equilibrium mixture of two isomeric cis pairs which, as in the case of symmetrical 1,3‐diphenyltriazenes, undergo thermal cis‐to‐trans isomerization by means of 1,3‐prototropic rearrangements catalyzed by general acids and general bases. A quantitative analysis, by means of a multiple‐substituent Hammett equation, of the rate constants for restricted rotation around the N‐2—N‐3 bond in cis‐1,3‐diphenyltriazenes renders ρ values of −1.93±0.08 and 0.82±0.08 for N‐1 and N‐3, respectively. Copyright © 2005 John Wiley & Sons, Ltd.
Inferring ideal amino acid interaction forms from statistical protein contact potentials
Authors: Pokarowski Piotr , Kloczkowski Andrzej , Jernigan Robert L. , Kothari Neha S. , Pokarowska Maria , Kolinski Andrzej 
Published: February 2005

AbstractWe have analyzed 29 different published matrices of protein pairwise contact potentials (CPs) between amino acids derived from different sets of proteins, either crystallographic structures taken from the Protein Data Bank (PDB) or computer‐generated decoys. Each of the CPs is similar to 1 of the 2 matrices derived in the work of Miyazawa and Jernigan (Proteins 1999;34:49–68). The CP matrices of the first class can be approximated with a correlation of order 0.9 by the formula eij = hi + hj, 1 ≤ i, j ≤ 20, where the residue‐type dependent factor h is highly correlated with the frequency of occurrence of a given amino acid type inside proteins. Electrostatic interactions for the potentials of this class are almost negligible. In the potentials belonging to this class, the major contribution to the potentials is the one‐body transfer energy of the amino acid from water to the protein environment. Potentials belonging to the second class can be approximated with a correlation of 0.9 by the formula eij = c0 − hihj + qiqj, where c0 is a constant, h is highly correlated with the Kyte–Doolittle hydrophobicity scale, and a new, less dominant, residue‐type dependent factor q is correlated (∼0.9) with amino acid isoelectric points pI. Including electrostatic interactions significantly improves the approximation for this class of potentials. While, the high correlation between potentials of the first class and the hydrophobic transfer energies is well known, the fact that this approximation can work well also for the second class of potentials is a new finding. We interpret potentials of this class as representing energies of contact of amino acid pairs within an average protein environment. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Protein domain of unknown function DUF1023 is an α/β hydrolase
Authors: Zheng Mingzhu , Ginalski Krzysztof , Rychlewski Leszek , Grishin Nick V. 
Published: February 2005

AbstractPfam family DUF1023 consists entirely of uncharacterized proteins generated by sequencing the genomes of Actinobacteria (Bateman A., et al., Nucleic Acids Res. 2004;32 Database issue:D138–141.) Utilizing sequence similarity detection methods, we infer homology between DUF1023 and α/β hydrolases. DUF1023 proteins conserve the core secondary structures in α/β hydrolase fold, and share similar catalytic machinery as that of α/β hydrolases. We predict DUF1023 spatial structure and deduce that they function as hydrolases utilizing catalytic Ser‐His‐Asp triad with the serine as a nucleophile. Proteins 2005. © 2005 Wiley‐Liss, Inc.
The human prion protein α2 helix: A thermodynamic study of its conformational preferences
Authors: Tizzano Barbara , Palladino Pasquale , De Capua Antonia , Marasco Daniela , Rossi Filomena , Benedetti Ettore , Pedone Carlo , Ragone Raffaele , Ruvo Menotti 
Published: February 2005

AbstractWe have synthesized both free and terminally‐blocked peptide corresponding to the second helical region of the globular domain of normal human prion protein, which has recently gained the attention of structural biologists because of a possible role in the nucleation process and fibrillization of prion protein. The profile of the circular dichroism spectrum of the free peptide was that typical of α‐helix, but was converted to that of β‐structure in about 16 h. Instead, below 2.1 × 10−5 M, the spectrum of the blocked peptide exhibited a single band centered at 200 nm, unequivocally associated to random conformations, which did not evolve even after 24 h. Conformational preferences of this last peptide have been investigated as a function of temperature, using trifluoroethanol or low‐concentration sodium dodecyl sulfate as α‐ or β‐structure inducers, respectively. Extrapolation of free energy data to zero concentration of structuring agent highlighted that the peptide prefers α‐helical to β‐type organization, in spite of results from prediction algorithms. However, the free energy difference between the two forms, as obtained by a thermodynamic cycle, is subtle (roughly 5–8 kJ mol−1 at any temperature from 280 K to 350 K), suggesting conformational ambivalence. This result supports the view that, in the prion protein, the structural behavior of the peptide is governed by the cellular microenvironment. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Polarization dynamics of microcavity polaritons: Three excitation regimes
Authors: Kłopotowski Ł. , Amo A. , Martín M. D. , Viña L. , André R. 
Published: February 2005

AbstractWe present the results of time‐resolved studies of polariton dynamics under non‐resonant, circularly polarized excitation. We show how the emission intensity, its decay rate and the polarization behavior change in three characteristic excitation regimes and discuss the underlying relaxation mechanisms. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Growth and continuous‐wave laser operation of disordered crystals of Yb3+:NaLa(WO4)2 and Yb3+:NaLa(MoO4)2
Authors: Liu J. , Cano‐Torres J. M. , Cascales C. , Esteban‐Betegón F. , Serrano M. D. , Volkov V. , Zaldo C. , Rico M. , Griebner U. , Petrov V. 
Published: February 2005

AbstractSingle crystals of disordered NaLa(WO4)2 and NaLa(MoO4)2 doped with Yb3+ are grown by the Czochralski method from the melt. Continuous‐wave laser operation with Ti:sapphire laser pumping is demonstrated at room temperature without special cooling. Tunability from 1017 to 1057 nm and from 1015 to 1053 nm is achieved for Yb:NaLa(WO4)2 and Yb:NaLa(MoO4)2, respectively. A maximum output power of 205 mW is obtained with Yb:NaLa(WO4)2. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Optical study of Langmuir–Schaeffer films of gold colloid nanoparticles
Authors: Nabok A. , Heriot S. Y. , Richardson T. H. 
Published: February 2005

AbstractThin films of 5 nm gold colloid nanoparticles were deposited onto solid substrates (silicon, glass, gold coated glass) by the Langmuir–Schaeffer (LS) method at a surface pressure of 10 mN/m. The films produced were characterised with optical techniques of UV–visible absorption spectroscopy, surface plasmon resonance (SPR), and spectroscopic ellipsometry. Film thickness was found to increase linearly with the increase in the number of layers, yielding the values of 2.5 nm and 5.2 nm per deposition stroke for LB and LS films, respectively. Gold colloid films produce SPR curves broadened and shifted to the larger angles in respect to SPR of evaporated gold, which may be related to the effect of quantum confinement of electrons in gold colloid particles. Fitting of both SPR and ellipsometry data yields the value of 7 nm for the Au particles size, which is close to the values obtained by AFM. We also report on the reduction in the effective thickness of evaporated gold films after depositing gold colloid on top. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Thin films of copper hexadecafluorophthalocyanine CuPcF16
Authors: Basova T. , Kol'tsov E. , Hassan A. , Tsargorodskaya A. , Ray A. , Igumenov I. 
Published: February 2005

AbstractIn this work, structural features and optical properties of CuPcF16 films deposited by physical vapour deposition have been investigated. Thin films of two different thicknesses (22 and 198 nm) were characterized by ellipsometry, optical absorption spectroscopy and scanning electron microscopy. Film morphology and optical properties are found to depend on film thickness. Absorption spectra of CuPcF16 films were compared with those of unsubstituted copper phthalocyanine. The sensor response of CuPcF16 film to ammonia was studied using surface plasmon resonance measurements. It was stated that strong electron‐withdrawing fluorine substituents make this compound sensitive to reducing gases such as NH3 while unsubstituted CuPc is practically insensitive to this gas. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)