bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prediction of the conformation and geometry of loops in globular proteins: Testing ArchDB, a structural classification of loops
Authors: Fernandez‐Fuentes Narcis , Querol Enrique , Aviles Francesc X. , Sternberg Michael J. E. , Oliva Baldomero 
Published: July 2005

AbstractIn protein structure prediction, a central problem is defining the structure of a loop connecting 2 secondary structures. This problem frequently occurs in homology modeling, fold recognition, and in several strategies in ab initio structure prediction. In our previous work, we developed a classification database of structural motifs, ArchDB. The database contains 12,665 clustered loops in 451 structural classes with information about ϕ–ψ angles in the loops and 1492 structural subclasses with the relative locations of the bracing secondary structures. Here we evaluate the extent to which sequence information in the loop database can be used to predict loop structure. Two sequence profiles were used, a HMM profile and a PSSM derived from PSI‐BLAST. A jack‐knife test was made removing homologous loops using SCOP superfamily definition and predicting afterwards against recalculated profiles that only take into account the sequence information. Two scenarios were considered: (1) prediction of structural class with application in comparative modeling and (2) prediction of structural subclass with application in fold recognition and ab initio. For the first scenario, structural class prediction was made directly over loops with X‐ray secondary structure assignment, and if we consider the top 20 classes out of 451 possible classes, the best accuracy of prediction is 78.5%. In the second scenario, structural subclass prediction was made over loops using PSI‐PRED (Jones, J Mol Biol 1999;292:195–202) secondary structure prediction to define loop boundaries, and if we take into account the top 20 subclasses out of 1492, the best accuracy is 46.7%. Accuracy of loop prediction was also evaluated by means of RMSD calculations. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Main‐chain conformational tendencies of amino acids
Authors: Anderson Robert J. , Weng Zhiping , Campbell Robert K. , Jiang Xuliang 
Published: July 2005

AbstractA Ramachandran plot is a visual representation of the main‐chain conformational tendencies of an amino acid. Despite forty years of research, the shape of Ramachandran plots is still a matter of debate. The issue in making a Ramachandran plot based on experimental data is deciding whether sparse data represent genuine conformations. We present here a simple solution to settle the ambiguities of the sparse data, and explain how we verified the accuracies of our plots using an independent dataset. To obtain our results, we then measured the pair‐wise distances of main‐chain conformational tendencies among amino acids, and showed that the conformational relationships of amino acids are well preserved in a two‐dimensional map, leading to the conclusion that the conformational diversity space of amino acids is largely two dimensional. We further noticed that amino acids in early and late evolutionary stages are located in different zones in the two‐dimensional map. In addition to these conclusions, we here present an amino acid substitution table derived from experimental data. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Hybrid native partitioning of interactions among nonconserved residues in chimeric proteins
Authors: Hernández Griselda , LeMaster David M. 
Published: July 2005

AbstractGiven any operational criterion for pairwise interatomic interactions, for a pair of structurally homologous proteins there exists for both proteins a unique equivalent partitioning of the nonconserved residue positions into mutually non‐interacting clusters. In the formation of a chimeric protein derived from these two parental sequences, if nonnative‐like interactions are to be avoided in its tertiary structure, then all of the nonconserved residues of each cluster must necessarily be either maintained or interchanged simultaneously. This hybrid native partitioning criterion is applied to known gene shuffling results. When the degree of estimated disruption is modest, the HybNat algorithm provides an efficient predictor of structural integrity. This supports the expectation that a substantial fraction of sequences that conform to the hybrid native partitioning criterion will yield tertiary structures that largely preserve the native‐like interactions of the parental proteins. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Structural analysis of a set of proteins resulting from a bacterial genomics project
Authors: Badger J. , Sauder J.M. , Adams J.M. , Antonysamy S. , Bain K. , Bergseid M.G. , Buchanan S.G. , Buchanan M.D. , Batiyenko Y. , Christopher J.A. , Emtage S. , Eroshkina A. , Feil I. , Furlong E.B. , Gajiwala K.S. , Gao X. , He D. , Hendle J. , Huber A. , Hoda K. , Kearins P. , Kissinger C. , Laubert B. , Lewis H.A. , Lin J. , Loomis K. , Lorimer D. , Louie G. , Maletic M. , Marsh C.D. , Miller I. , Molinari J. , Muller‐Dieckmann H.J. , Newman J.M. , Noland B.W. , Pagarigan B. , Park F. , Peat T.S. , Post K.W. , Radojicic S. , Ramos A. , Romero R. , Rutter M.E. , Sanderson W.E. , Schwinn K.D. , Tresser J. , Winhoven J. , Wright T.A. , Wu L. , Xu J. , Harris T.J.R. 
Published: July 2005

AbstractThe targets of the Structural GenomiX (SGX) bacterial genomics project were proteins conserved in multiple prokaryotic organisms with no obvious sequence homolog in the Protein Data Bank of known structures. The outcome of this work was 80 structures, covering 60 unique sequences and 49 different genes. Experimental phase determination from proteins incorporating Se‐Met was carried out for 45 structures with most of the remainder solved by molecular replacement using members of the experimentally phased set as search models. An automated tool was developed to deposit these structures in the Protein Data Bank, along with the associated X‐ray diffraction data (including refined experimental phases) and experimentally confirmed sequences. BLAST comparisons of the SGX structures with structures that had appeared in the Protein Data Bank over the intervening 3.5 years since the SGX target list had been compiled identified homologs for 49 of the 60 unique sequences represented by the SGX structures. This result indicates that, for bacterial structures that are relatively easy to express, purify, and crystallize, the structural coverage of gene space is proceeding rapidly. More distant sequence‐structure relationships between the SGX and PDB structures were investigated using PDB‐BLAST and Combinatorial Extension (CE). Only one structure, SufD, has a truly unique topology compared to all folds in the PDB. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Co‐translational myristoylation alters the quaternary structure of HIV‐1 Nef in solution
Authors: Dennis Caitríona A. , Baron Andrew , Grossmann J. Günter , Mazaleyrat Sabine , Harris Mark , Jaeger Joachim 
Published: July 2005

AbstractWe have studied the solution properties of Nef, a 24‐kDa cotranslationally myristoylated protein produced by HIV‐1 and other primate lentiviruses. Nef is found in the cytosol and also in association with cytoplasmic membranes, the latter, mediated in part by the myristoyl group attached to the N‐terminal glycine. Recombinant Nef was coexpressed in Escherichia coli in tandem with N‐myristoyl‐transferase and is fully myristoylated. Analysis by circular dichroism showed the myristoylated form to contain a greater α‐helical content than the nonmyristoylated form. Analysis of modified and unmodified Nef in solution using small angle X‐ray scattering, dynamic laser light scattering and analytical ultracentrifugation consistently showed differences in the oligomeric states of the two forms of Nef. Myristoylated Nef is predominantly monomeric and small oligomers which are also present, can be converted to the monomeric form under reducing conditions. By contrast, the nonmyristoylated form exists as a stable hexadecamer in solution which disassociates into tetramers upon addition of reducing agents. Shape reconstructions from small angle scattering curves of nonmyristoylated Nef are compatible with a large disc‐like structure in the hexadecameric oligomer consisting of four Nef tetramers. From these findings, we hypothesize that Nef undergoes a substantial conformational change from an “open” into a “closed” form whereby the myristate group is sequestered in a hydrophobic pocket. The myristoylated protein can switch to the open conformation by association of the N‐terminal region of molecule with membranes. These changes would allow Nef to carry out various functions depending on the conformational and oligomeric states. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Statistical characterization of salt bridges in proteins
Authors: Sarakatsannis James N. , Duan Yong 
Published: July 2005

AbstractThe structure and folding mechanism of a given protein are determined by many factors, including the electrostatic interactions between charged residues of protein molecules known in general as salt bridges. In this study, analyses were conducted on 10,370 salt bridges in 2017 proteins and the results compared to previous statistical surveys of 36 protein structures. Although many of the general trends remained consistent with other studies, more detailed information was illuminated by the larger dataset. In particular, it was shown that there is a strong correlation between secondary structure and salt bridge formation, and that salt bridges display preferential formation in an environment of about 30% solvent accessible surface area. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Comparative analysis of amino acid distributions in integral membrane proteins from 107 genomes
Authors: Nilsson Johan , Persson Bengt , von Heijne Gunnar 
Published: July 2005

AbstractWe have performed a comparative analysis of amino acid distributions in predicted integral membrane proteins from a total of 107 genomes. A procedure for identification of membrane spanning helices was optimized on a homology‐reduced data set of 170 multi‐spanning membrane proteins with experimentally determined topologies. The optimized method was then used for extraction of highly reliable partial topologies from all predicted membrane proteins in each genome, and the average biases in amino acid distributions between loops on opposite sides of the membrane were calculated. The results strongly support the notion that a biased distribution of Lys and Arg residues between cytoplasmic and extra‐cytoplasmic segments (the positive‐inside rule) is present in most if not all organisms. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Effect of thickness and cold substrate on transport properties of thermally evaporated CdTe thin films
Authors: El‐Mongy A. Abd , Hashem H. M. , Ramadan A. A. 
Published: July 2005

AbstractThe correlation between the structural characteristics (stoichiometry and crystallite size) of CdTe films and their electronic transport properties were the aims of the present study to bring attention to the dual importance of grain size and conversion of the semiconductivity type with changing film thickness. Two main parameters were considered: the substrate temperature and film thickness. Transport properties were influenced by grain boundaries as well as by native doping. Optical measurements showed two main direct transitions at energies: E1 ≈ 1.55 eV (fundamental gap) and E2 ≈ 2.49 eV (due to valence band splitting). Both transitions were found to be thickness dependent with a marked change at a film thickness of about 300 nm. In the case of low substrate temperature, the scaling relation between resistivity and grain size showed a deviation from linear behavior at a size of 20 nm and the transmission coefficient is reduced. Also, the deposition on cold substrate enhanced both dark and photoconductivity for films of thickness ≥300 nm. It is also proved that the carrier transport was affected by the transmission coef‐ficient for carriers to pass a single grain boundary as well as the number of grain boundaries per mean free path. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Hall effect of copper nitride thin films
Authors: Yue G. H. , Liu J. Z. , Li M. , Yuan X. M. , Yan P. X. , Liu J. L. 
Published: July 2005

AbstractThe Hall effect of copper nitride (Cu3N) thin films was investigated in our work. Cu3N films were deposited on glass substrates by radio‐frequency (RF) magnetron sputtering at different temperatures using pure copper as the sputtering target. The Hall coefficients of the films are demonstrated to be dependent on the deposition gas flow rate and the measuring temperature. Both the Hall coefficient and resistance of the Cu3N films increase with the nitrogen gas flow rate at room temperature, while the Hall mobility and the carrier density of the films decrease. As the temperature changed from 100 K to 300 K, the Hall coefficient and the resistivity of the films decreased, while the carrier density increased and Hall mobility shows no great change. The energy band gap of the Cu3N films deduced from the curve of the common logarithm of the Hall coefficient against 1/T is 1.17–1.31 eV. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
TEM observation on the microstructure of Co doped C films
Authors: Mi W. B. , Li Z. Q. , Wu P. , Jiang E. Y. , Bai H. L. 
Published: July 2005

AbstractCo doped C films with different Co volume fraction xv were fabricated using facing‐target sputtering at room temperature. The as‐deposited films are composed of ∼2 nm amorphous Co granules dispersed in a‐C matrix, and their morphology is composition independent. The graphitized carbon nanostructure appears in the as‐deposited C films (xv = 43) after being irradiated by electron beam for several minutes. Annealing at 300–450 °C causes the crystallization of amorphous Co followed by an increase of grain size. The constrictions arising from the structural environment result in the coexistence of the hcp and fcc Co phases at temperatures higher than the phase transformation point of 425 °C. Annealed at 650 °C, crystalline Co particles transform into hcp structure with stacking faults and amorphous C graphitizes. The graphite (002) lattice in the annealed C films preferentially grows up on the surface of Co particles. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
High purity alpha silicon nitride nanowires – synthesis and dielectric properties
Authors: Xie T. , Wu Y. C. , Cai W. P. , Zhang L. D. 
Published: July 2005

AbstractHigh purity single crystal alpha silicon nitride (α‐Si3N4) nanowires were obtained in high yield via a simple vapor phase reaction approach without the presence of catalyst. The produced α‐Si3N4 nanowires have diameters mostly ranging from 30 to 100 nm and lengths of several hundred micrometers. The nanowires were grown via vapor–solid (VS) mechanism. The room‐temperature dielectric properties show that the effective dielectric constants of α‐Si3N4 nanowires is higher than that of the α‐Si3N4 micropowders, especially at low frequencies. Analysis of the dielectric properties indicates that the small size effect of nanowires has great influence on the dielectric behavior of the samples. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The role of interfaces on the magnetic behavior of granular CuFeCo alloys
Authors: Ghafari M. , Volland A. , Hahn H. 
Published: July 2005

AbstractGranular thin films of face centered tetragonal (fct) FeCo‐clusters in a γ‐CuCo matrix show a giant magneto resistance effect. Cu100–x(Fe50Co50)x samples with 63 ≤ x ≤ 88 were examined using Mössbauer Spectroscopy, electron microscopy, Magnetoresistance, SQUID and Rutherford Backscattering Spectroscopy. In ultrafine particles with fct‐FeCo imbedded in a CuCo matrix the giant magneto resistance effect is strongly correlated to the ratio of interface/bulk. The magnetic interfaces form an additional scattering centere for the electrons which causes an increase of the GMR effect. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim )
Polariton correlation in microcavities produced by parametric scattering
Authors: Langbein Wolfgang 
Published: July 2005

AbstractThe spontaneous and self‐stimulated parametric emission from a semiconductor microcavity after resonant pulsed excitation is measured. The emission of the lower polariton branch is resolved in two‐dimensional momentum space, using either time‐resolved or spectrally resolved detection. The polariton–polariton scattering dynamics is generally in good agreement with the theory using the nonlinearity due to the excitonic part and the dispersion due to the photonic part of the polariton. The peculiar figure‐8 shaped distribution in momentum space of the final states of the parametric scattering is observed. Renormalization of the dispersion due to the bound biexciton state is found to influence the final state distribution. Using two pump directions the shape of the final state distribution can be changed to a peanut or oval for the mixed parametric processes. In this dual pump configuration, we find that polaritons in two distinct idler‐modes interfere if and only if they share the same signal‐mode, showing the existence of polariton pair correlations that store the “which‐way” information. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Microcavities in Ecole Polytechnique Fédérale de Lausanne, Ecole Polytechnique (France) and elsewhere: past, present and future
Authors: Weisbuch Claude , Benisty Henri 
Published: July 2005

AbstractWe present an overview of semiconductor microcavity research, with emphasis on the activities carried out at Ecole Polytechnique Fédérale de Lausanne and Ecole Polytechnique (Palaiseau, France). (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Discrimination between diastereoisomeric dipeptides by IR–UV double resonance spectroscopy and ab initio calculations
Authors: Abo‐Riziq Ali G. , Bushnell John E. , Crews Bridgit , Callahan Michael P. , Grace Louis , De Vries Mattanjah S. 
Published: July 2005

AbstractWe studied diastereoisomeric dipeptides, containing two chiral centers, by comparing ab initio calculations with laser desorption jet‐cooling experiments. We studied the hetero‐dipeptides LL–VF (L‐Val‐L‐Phe) and DL–VF and the homo‐dipeptides LL–FF (L‐Phe‐L‐Phe) and LD–FF. Changing one of the chiral centers in each molecule leads to changes in the spectra that can be used to distinguish between diastereoisomeric pairs. We observed three different conformers for LL–VF, four for DL–VF, two for LL–FF, and one for LD–FF. By comparing the results from IR–UV double resonant spectroscopy with ab initio calculations, we can draw conclusions about the conformational structures. At the same time, the experimental data serve as a test for the computational results. We discuss the possibilities and limitations of the interplay between theory and experiment. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005
Structure and nonlinear optical properties of the HMT–CDA 1:1 adduct: Experimental and DFT approach
Authors: Venkatraman Ramaiyer , Ray Paresh Chandra , Fronczek Frank R. , Singh Jagdish P. 
Published: July 2005

AbstractEquimolar amounts of hexamethylenetetramine (HMT) and trans‐1,2‐cyclohexanedicarboxylic acid (CDA) formed a self‐assembled unit through a hydrogen bonding network. Room temperature single‐crystal diffraction studies and Fourier transform infrared (FTIR) spectroscopy of the system indicated adduct formation between HMT and CDA. The crystalline adduct sample exhibited appreciable macroscopic nonlinear optical (NLO) properties. Density functional theory (DFT) calculations, using the 6‐31G(d,p) basis set, have been performed to investigate the gas‐phase structure and IR frequencies. The dynamic NLO properties were calculated with the ZINDO/CV method, including solvent effects. Theoretical parameters (geometry and vibrational frequencies) predicted by the DFT method for the adduct are in good agreement with the experimental data. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005
Analysis of aflatoxin B1‐lysine adduct in serum using isotope‐dilution liquid chromatography/tandem mass spectrometry
Authors: McCoy Leslie F. , Scholl Peter F. , Schleicher Rosemary L. , Groopman John D. , Powers Carissa D. , Pfeiffer Christine M. 
Published: July 2005

AbstractA method for quantitative analysis of aflatoxin B1‐lysine adduct (B1‐Lys) in serum by liquid chromatography using tandem mass spectrometry (LC/MS/MS) is presented. The protein in a 250‐µL sample was digested in the presence of a stable‐isotope internal standard during a 4‐h incubation at 37°C with Pronase™. B1‐Lys and the internal standard were extracted using mixed‐mode solid‐phase extraction cartridges and eluted with 2% formic acid in methanol. Following evaporation and reconstitution, extracts were injected onto a Luna C‐18(2) column and eluted with a step gradient of acetonitrile and 0.06% formic acid. The B1‐Lys and the internal standard were detected in a positive ionization selective reaction monitoring mode with a ThermoFinnigan TSQ Quantum triple quadrupole mass spectrometer. Calibration curves were linear for concentrations from 0.05–8.0 ng/mL. The method was validated with aflatoxin B1 dosed rat serum diluted to anticipated high and low concentrations. Total imprecision determined from 30 measurements over 15 days was 5.6% and 9.1%, respectively. Recoveries of 78.8 ± 6.4% for B1‐Lys and 85.4 ± 12.4% for the internal standard were based on the full extraction and reconstitution processes. The method can be used to quantitate B1‐Lys at the 0.5 pg/mg albumin level and is suitable for routine analysis. Copyright © 2005 John Wiley & Sons, Ltd.
Application of positive ion chemical ionisation and tandem mass spectrometry combined with gas chromatography to the trace level analysis of ethyl carbamate in bread
Authors: Hamlet Colin G. , Jayaratne Sanal M. , Morrison Carol 
Published: July 2005

AbstractA rapid, sensitive and selective method has been developed and validated for the analysis of the contaminant ethyl carbamate (EC) in bread products at the part‐per‐billion level. The new procedure uses positive ion chemical ionisation (PICI) and tandem mass spectrometry (MS/MS), combined with gas chromatography (GC), on a ‘bench‐top’ triple‐quadrupole mass spectrometer. Ammonia was the PICI reagent gas of choice because of its ability to produce abundant [M+H]+ and [M+NH4]+ ions from EC and deuterium‐labelled EC (LEC) used as an internal standard. For identification and quantification, selected reaction monitoring (SRM) was used to follow the precursor‐to‐product ion transitions of m/z 107 → 90, m/z 107 → 62 and m/z 90 → 62 for EC, as well as m/z 112 → 63 for the LEC internal standard. The limits of detection and quantification were 0.6 and 1.2 µg kg−1, respectively, and the recovery of the method was 101 ± 10% at 10 µg kg−1 and 98 ± 5% at 100 µg kg−1. The precision of the method, established under conditions of intermediate reproducibility, did not exceed a relative standard deviation of 7%. The quantitative performance of the new GC/PICI‐SRM procedure compared favourably with that of a reference method based on GC/MS and selected ion monitoring (correlation coefficient, r = 0.997). However, the new method had the advantages of reduced sample preparation time, improved sensitivity and unambiguous identification of EC at all concentrations. Application of the new method to the analysis of 50 UK breads showed that levels of EC ranged from 0.6 to 2.3 µg kg−1 in retail products and from 3.1 to 12.2 µg kg−1 for breads prepared using domestic breadmaking machines (dry weight basis). Toasting bread in a domestic toaster led to increases of between two‐ and three‐fold in mean EC concentrations. Copyright © 2005 John Wiley & Sons, Ltd.