bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome‐wide transcriptomic and proteomic analysis of the primary response to phosphate limitation in Streptomyces coelicolor M145 and in a ΔphoP mutant
Authors: Rodríguez‐García Antonio , Barreiro Carlos , Santos‐Beneit Fernando , Sola‐Landa Alberto , Martín Juan F. 
Published: July 2007

AbstractPhosphate limitation in Streptomyces and in other bacteria triggers expression changes of a large number of genes. This response is mediated by the two‐component PhoR–PhoP system. A Streptomyces coelicolor ΔphoP mutant (lacking phoP) has been obtained by gene replacement. A genome‐wide analysis of the primary response to phosphate limitation using transcriptomic and proteomic studies has been made in the parental S. coelicolor M145 and in the ΔphoP mutant strains. Statistical analysis of the contrasts between the four sets of data generated (two strains under two phosphate conditions) allowed the classification of all genes into 12 types of profiles. The primary response to phosphate limitation involves upregulation of genes encoding scavenging enzymes needed to obtain phosphate from different phosphorylated organic compounds and overexpression of the high‐affinity phosphate transport system pstSCAB. Clear interactions have been found between phosphate metabolism and expression of nitrogen‐regulated genes and between phosphate and nitrate respiration genes. PhoP‐dependent repressions of antibiotic biosynthesis and of the morphological differentiation genes correlated with the observed ΔphoP mutant phenotype. Bioinformatic analysis of the presence of PHO boxes (PhoP‐binding sequences) in the upstream regions of PhoP‐controlled genes were validated by binding of PhoP, as shown by electrophoretic mobility shift assays.
Proteome analysis and characterization of phenotypes of lesion mimic mutantspotted leaf 6in rice
Authors: Kang Sang Gu , Matin Mohammad Nurul , Bae Hanhong , Natarajan Savithiry 
Published: July 2007

AbstractRicespotted leaf 6(spl6) mutant produces lesions caused by spontaneous cell death in the absence of pathogenic infection. Expression of this genetic trait was developmentally programmed. After the tillering stage, small red and brown lesions were initiated in groups on the leaf blade. Eventually, the lesions formed parallel lines along the midrib of the leaf. Under light and transmission electron microscopy, we observed that thylakoid membranes of mesophyll chloroplasts were progressively damaged in the nonspotted section of the mutant leaf. However, chloroplasts were absent in the mesophyll cells of the spotted area of thespl6mutant. These results indicated that lesion formation of thespl6mutant might be caused by oxidative burst. Proteome analysis revealed that 159 protein spots were up or downregulated in comparison between spotted leaves of thespl6mutant plants and normal leaves of the wild type. Among them, protein disulfide isomerase (PDI), transketolase, thioredoxin peroxidase (TPX), ATP synthase, RuBisCO large subunit, and RuBisCO activase small subunit were not identified in thespl6mutant but were abundant in the wild type. Especially, the absence of TPX and PDI might be the cause of the failure to protect cells against oxidative burst resulting in degradation of the thylakoid membranes and leading to programmed cell death and lesion development.
Proteomic analysis of plasma membrane lipid rafts of HL‐60 cells
Authors: Yanagida Mitsuaki , Nakayama Hitoshi , Yoshizaki Fumiko , Fujimura Tsutomu , Takamori Kenji , Ogawa Hideoki , Iwabuchi Kazuhisa 
Published: July 2007

AbstractNeutrophils acquire phagocytic activity as they differentiate. Recently, plasma membrane lipid rafts have been shown to play important roles in the process of phagocytosis in neutrophils. To characterize the proteins involved in phagocytosis and to elucidate the process by which they acquire phagocytic activity, we investigated by nano‐LC‐MS/MS analysis the changes in protein composition of plasma membrane lipid rafts during DMSO‐induced differentiation of the human leukemia cell line HL‐60 cells into neutrophilic lineage. Based on the spectrum counts of 147 proteins identified, 25 proteins were upregulated and 49 were downregulated by DMSO treatment. CD11b/CD18 subunits of β2‐integrin Mac‐1, CD35, and GPI‐80, which are known to be upregulated during differentiation, were dominantly detected in the lipid rafts of DMSO‐treated cells. Many known membrane proteins, G proteins, and cytoskeletal proteins were also detected and they showed characteristic distributions. Absolute quantification of nine proteins in the lipid rafts using internal standard peptides labeled with stable isotopes showed that the amount of protein almost corresponded to the results obtained by spectrum count. Identified proteins, expression of which was altered by DMSO treatment, are expected to be candidate proteins involved in differentiation and functions of neutrophils.
Proteomics of nipple aspirate fluid, breast cyst fluid, milk, and colostrum
Authors: Ruhlen Rachel L. , Sauter Edward R. 
Published: July 2007

AbstractProteomic analysis of breast fluids has wide‐ranging clinical applications. Protein expression in nipple aspirate fluid and breast cyst fluid may prove valuable for the detection and monitoring of breast cancer, but has been hampered by the lack of a single marker with sufficient breast cancer sensitivity and specificity to be clinically useful. The assessment of multiple proteins may offer a more powerful cancer detection tool. Breast cancer is particularly difficult to detect in women who are lactating. The identification of cancer predicting proteins in milk may prove very helpful in an early cancer detection in this group of women. A better understanding of the protein composition of milk and colostrum should improve infant care and nutrition, and lead to alternatives for individuals with milk allergies.
Common conformational changes in flavodoxins induced by FMN and anion binding: The structure of Helicobacter pylori apoflavodoxin
Authors: Martínez‐Júlvez Marta , Cremades Nunilo , Bueno Marta , Pérez‐Dorado Inmaculada , Maya Celia , Cuesta‐López Santiago , Prada Diego , Falo Fernando , Hermoso Juan A. , Sancho Javier 
Published: July 2007

AbstractFlavodoxins, noncovalent complexes between apoflavodoxins and flavin mononucleotide (FMN), are useful models to investigate the mechanism of protein/flavin recognition. In this respect, the only available crystal structure of an apoflavodoxin (that from Anabaena) showed a closed isoalloxazine pocket and the presence of a bound phosphate ion, which posed many questions on the recognition mechanism and on the potential physiological role exerted by phosphate ions. To address these issues we report here the X‐ray structure of the apoflavodoxin from the pathogen Helicobacter pylori. The protein naturally lacks one of the conserved aromatic residues that close the isoalloxazine pocket in Anabaena, and the structure has been determined in a medium lacking phosphate. In spite of these significant differences, the isoallozaxine pocket in H. pylori apoflavodoxin appears also closed and a chloride ion is bound at a native‐like FMN phosphate site. It seems thus that it is a general characteristic of apoflavodoxins to display closed, non‐native, isoalloxazine binding sites together with native‐like, rather promiscuous, phosphate binding sites that can bear other available small anions present in solution. In this respect, both binding energy hot spots of the apoflavodoxin/FMN complex are initially unavailable to FMN binding and the specific spot for FMN recognition may depend on the dynamics of the two candidate regions. Molecular dynamics simulations show that the isoalloxazine binding loops are intrinsically flexible at physiological temperatures, thus facilitating the intercalation of the cofactor, and that their mobility is modulated by the anion bound at the phosphate site. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Protonation state and substrate binding to B2 metallo‐β‐lactamase CphA from Aeromonas hydrofila
Authors: Simona F. , Magistrato A. , Vera D. M. A. , Garau G. , Vila A. J. , Carloni P. 
Published: July 2007

AbstractThe zinc enzymes metallo β‐lactamases counteract the beneficial action of β‐lactam antibiotics against bacterial infections, by hydrolyzing their β‐lactam rings. To understand structure/function relationships on a representative member of this class, the B2 MβL CphA, we have investigated the H‐bond pattern at the Zn enzymatic active site and substrate binding mode by molecular simulation methods. Extensive QM calculations at the DFT‐BLYP level on eleven models of the protein active site, along with MD simulations of the protein in aqueous solution, allow us to propose two plausible protonation states for the unbound enzyme, which are probably in equilibrium. Docking procedures along with MD simulations and QM calculations suggest that in the complex between the enzyme and its substrate (biapenem), the latter is stable in only one of the two protonation states, in addition it exhibits two different binding modes, of which only one agrees with previous proposals. In both cases, the substrate is polarized as in aqueous solution. We conclude that addressing mechanistic issues on this class of enzymes requires a careful procedure to assign protonation states and substrate docking modes. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Substrate polarization in enzyme catalysis: QM/MM analysis of the effect of oxaloacetate polarization on acetyl‐CoA enolization in citrate synthase
Authors: van der Kamp Marc W. , Perruccio Francesca , Mulholland Adrian J. 
Published: July 2007

AbstractCitrate synthase is an archetypal carbon–carbon bond forming enzyme. It promotes the conversion of oxaloacetate (OAA) to citrate by catalyzing the deprotonation (enolization) of acetyl‐CoA, followed by nucleophilic attack of the enolate form of this substrate on OAA to form a citryl‐CoA intermediate and subsequent hydrolysis. OAA is strongly bound to the active site and its α‐carbonyl group is polarized. This polarization has been demonstrated spectroscopically, [(Kurz et al., Biochemistry 1985;24:452–457; Kurz and Drysdale, Biochemistry 1987;26:2623–2627)] and has been suggested to be an important catalytic strategy. Substrate polarization is believed to be important in many enzymes. The first step, formation of the acetyl‐CoA enolate intermediate, is thought to be rate‐limiting in the mesophilic (pig/chicken) enzyme. We have examined the effects of substrate polarization on this key step using quantum mechanical/molecular mechanical (QM/MM) methods. Free energy profiles have been calculated by AM1/CHARMM27 umbrella sampling molecular dynamics (MD) simulations, together with potential energy profiles. To study the influence of OAA polarization, profiles were calculated with different polarization of the OAA α‐carbonyl group. The results indicate that OAA polarization influences catalysis only marginally but has a larger effect on intermediate stabilization. Different levels of treatment of OAA are compared (MM or QM), and its polarization in the protein and in water analyzed at the B3LYP/6‐31+G(d)/CHARMM27 level. Analysis of stabilization by individual residues shows that the enzyme mainly stabilizes the enolate intermediate (not the transition state) through electrostatic (including hydrogen bond) interactions: these contribute much more than polarization of OAA. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Structural assessment of glycyl mutations in invariantly conserved motifs
Authors: Prakash Tulika , Sandhu Kuljeet Singh , Singh Nitin Kumar , Bhasin Yasha , Ramakrishnan C. , Brahmachari Samir K. 
Published: July 2007

AbstractMotifs that are evolutionarily conserved in proteins are crucial to their structure and function. In one of our earlier studies, we demonstrated that the conserved motifs occurring invariantly across several organisms could act as structural determinants of the proteins. We observed the abundance of glycyl residues in these invariantly conserved motifs. The role of glycyl residues in highly conserved motifs has not been studied extensively. Thus, it would be interesting to examine the structural perturbations induced by mutation in these conserved glycyl sites. In this work, we selected a representative set of invariant signature (IS) peptides for which both the PDB structure and mutation information was available. We thoroughly analyzed the conformational features of the glycyl sites and their local interactions with the surrounding residues. Using Ramachandran angles, we showed that the glycyl residues occurring in these IS peptides, which have undergone mutation, occurred more often in the L‐disallowed as compared with the L‐allowed region of the Ramachandran plot. Short range contacts around the mutation site were analyzed to study the steric effects. With the results obtained from our analysis, we hypothesize that any change of activity arising because of such mutations must be attributed to the long‐range interaction(s) of the new residue if the glycyl residue in the IS peptide occurred in the L‐allowed region of the Ramachandran plot. However, the mutation of those conserved glycyl residues that occurred in the L‐disallowed region of the Ramachandran plot might lead to an altered activity of the protein as a result of an altered conformation of the backbone in the immediate vicinity of the glycyl residue, in addition to long range effects arising from the long side chains of the new residue. Thus, the loss of activity because of mutation in the conserved glycyl site might either relate to long range interactions or to local perturbations around the site depending upon the conformational preference of the glycyl residue. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Truncated prolyl oligopeptidase from Pyrococcus furiosus
Authors: Juhász Tünde , Szeltner Zoltán , Polgár László 
Published: July 2007

AbstractThe peptidase domain of prolyl oligopeptidase is covered by a propeller domain, which excludes large peptides and proteins from the catalytic triad. Previous studies indicated that some amino acids of the N‐terminal region constitute a part of the substrate entrance to the active site. To investigate the catalytic role of the N‐terminus, we removed the residues 1–32 from the enzyme and examined the kinetic, thermodynamic, and structural consequences of the deletion, using the thermophile Pyrococcus furiosus prolyl oligopeptidase. An about threefold decrease in the catalytic activity along with a 20°C reduction in the temperature optimum was observed. The pH‐rate profile, the rate‐limiting step, and the activation parameters did not change significantly. However, a substantial decrease was observed in the stability of the protein as demonstrated by circular dichroism and differential scanning calorimetry measurements, and by denaturation with guanidinium chloride. It was concluded that the N‐terminal segment did not facilitate the substrate binding, independent of the size of the substrate, but contributed principally to the protein stability required for the formation of the proper active site. Proteins 2007. © 2007 Wiley‐Liss, Inc.
The Heat Capacity of Solid CF4
Authors: Bagatskii M. I. , Manzhelii V. G. , Popov V. A. 
Published: July 2007

AbstractThe heat capacity of solid tetrafluoromethane has been measured in the temperature range 2 to 20 °K. The analysis of the results of this paper and literature data on the heat capacity allow to make conclusions about the character of the heat motion of the molecules in crystalline CF4. An “extra” heat capacity of CF4 near the phase transformation temperature Tλ = 76.09 °K is due to orientational disordering. The temperature dependence of the “extra” heat capacity ΔCor is well described by the logarithmic function ΔCor ∼ lg ∼|–T|Tλ|.
Mössbauer Effect Study of the Structure of Inorganic Glasses
Authors: Bartenev G. M. , Suzdalev I. P. , Tsyganov A. D. 
Published: July 2007

AbstractThe structure of inorganic glasses and glass fibres has been investigated by means of the Mössbauer effect. According to Mössbauer effect data the microstructure of glass differs considerably from that of the glass fibre. The polymeric constitution of the glass is observed to undergo certain structural orientation during drawing of glass fibres which is indicated by the presence of an axially symmetrical molecular field, asymmetry of atom oscillations, and considerably lower degree of microheterogeneities. Heat treatment of glass fibres removes structural orientation. Tin ions, like other elements of the IVth group of the Mendeleev periodic table, can act as well as a glass former.
On Acoustic Attenuation in Dielectric Solids
Authors: Ožvold M. 
Published: July 2007

AbstractStarting from the general equation of motion for the atoms of the primitive lattice and using the Green function method the sound absorption coefficient is derived in the three‐phonon approximation. The here derived results hold for transverse waves in the whole frequency region and for longitudinal ones in the high frequency region (Ω τ > 1). The frequency and temperature dependence of the absorption coefficient are discussed for the high and low frequencies (Ω τ 1 and Ω τ 1). Using the dispersion relation, the change of elastic constants due to the three‐phonon processes is determined.
The Order — Disorder Transformation in Fe3Al Alloys
Authors: Lesoille M. R. , Gielen P. M. 
Published: July 2007

AbstractA Mössbauer investigation in FeAl alloys ranging from 20 to 28 at% Al has been performed. In the disordered spectra, which were computer analyzed, a very slight mean electric quadrupole interaction has been measured, which may be due to some directional order, while in the ordered spectra two ordered phases were observed for a composition around 25 at% Al: the DO3‐type of ordered structure, in which each Al atom has eight Fe nearest neighbours and six Fe next‐nearest neighbours, and another phase with a structure similar to Cu3Au, in which each Al atom has 12 Fe nearest neighbours and six Al next‐nearest neighbours. Both phases are ferromagnetic. In the Cu3Au‐type structure a strong electric quadrupole interaction has been measured, which is the same as in the Fe3AlC compound. The quadrupole effect does not appear in the DO3‐type structure probably because of special relationships between the easy axis of magnetization and the electric field gradient tensor. Measurements of quadrupole effects show that Al should be strongly ionized when alloyed with Fe. This gives a clue to understand the physical reasons why order‐disorder transitions appear in such alloys. Below the transition temperature, each Al gets better surrounded exclusively by Fe atoms in order to minimize the Coulomb interaction energy with its neighbours.
Spezifische Wärme und Debyetemperatur von AgCl zwischen 2 und 12 °K
Authors: Donecker J. 
Published: July 2007

AbstractDie spezifische Wärme wurde zwischen 2 und 12 °K gemessen. Die zugehörigen Debyetemperaturen werden angegeben und die Koeffizienten von ω2 und ω4 in der Entwicklung des Gitterspektrums für niedrige Frequenzen abgeschätzt. Für T → 0 ergibt sich eine Debyetemperatur von 162 (± 3) °K, die mit der elastischen Debyetemperatur Θel = 161,6 °K übereinstimmt. ΘC(T) hat in der Nähe von 10 °K ein Minimum. Das kann durch ein einfaches Modell für das Gitterspektrum erklärt werden, das eine Häufung von Moden bei ω ≈ 6,5 × 1012 s−1 enthält, die wahrscheinlich auf eine starke Dispersion transversaler akustischer Schwingungen zurückzuführen ist.
Second Harmonic Generation in Anisotropic Semiconductors Using DC Electric Fields
Authors: Sodha M. S. , Gupta B. M. 
Published: July 2007

AbstractAn analytical investigation is made of the use of dc electric fields of arbitrary strength for the generation of second harmonic of high frequency electromagnetic waves in anisotropic semiconductors. The acoustical phonon, non‐polar optical phonon, and intervalley scattering are assumed to be the dominant type of scattering. It is seen that for the frequency of wave much greater than the effective collision frequency (i.e. the IR region), the generated second harmonic is proportional to the applied dc field. This is in contrast to the case of microwave frequencies where the generation is most efficient at some optimum dc field. The calculations of the anisotropy and the magnitude of the second harmonic generated are reported for [100], [110], and [111] directions of the combined wave and dc field for the case of n‐Ge.
Elastic Diffusion Relaxation
Authors: Alefeld G. , Völkl J. , Schaumann G. 
Published: July 2007

AbstractA theory for relaxation strength and relaxation time of the elastic diffusion relaxation is derived. Strain relaxation, stress relaxation, and internal friction are considered. Interaction between the diffusing particles is taken into account. The behaviour of relaxation strength and relaxation time in the region of a critical point has been discussed. It is shown that at a critical point the static compressibility of the host lattice approaches infinity. Furthermore it is suggested, that the orientation and diffusion relaxation processes may cause strong dispersion and damping of phonons close to the Brillouin zone boundary.
Many‐Particle Approach to the Optical Absorption of the Alkali Metals
Authors: Stolz H. 
Published: July 2007

AbstractThe influence of the electron‐electron interaction on the optical absorption of the alkali metals is calculated in the ladder‐approximation for the Bethe‐Salpeter equation and in the nearly‐free‐electron approximation of the single‐particle functions. With a suitable approximation of the interaction matrix element the summation of an infinite number of ladder graphs is achieved. The resulting enhancement of the interband absorption — about 33% for sodium and 35% for potassium — is non‐resonant and there are no anomalous structures below the interband threshold.
On the Faraday Effect of Hot Electrons in Many‐Valley Semiconductors
Authors: Asche M. 
Published: July 2007

AbstractFor the calculation of the Faraday effect of hot electrons in many‐valley semiconductors the ellipsoidal form of the constant energy surfaces can be taken into account, if scattering between valleys on axes with different orientations to the applied fields is weak in comparison with other collision processes. In the case of small losses the rotation of the polarization plane and the ellipticity of radiation are discussed with respect to the electric de field as functions of mean carrier energies and electron redistribution among the valleys, considering interaction with acoustical and optical phonons as well as ionized impurities.
Energy Bands in β′‐PdIn
Authors: Cho S. J. 
Published: July 2007

AbstractThe energy bands for ordered β′‐PdIn have been calculated by the augmented‐plane‐wave (APW) method. The results are similar to those for β′‐CuZn except near R. The theoretical extremal Fermi surface cross‐sections are reasonably in agreement with those obtained by the de Haas‐van Alphen studies. The possible open orbits have also been studied. The electronic density of states curve has been obtained from the energy bands. The electronic specific heat coefficient, the magnetic susceptibility and the cyclotron effective masses have also been estimated. Comparisons have been made between our results and optical data.
Lattice Distortion in Uranium Dioxide near 30 °K
Authors: Pirie J. D. , Smith T. 
Published: July 2007

AbstractUranium dioxide is an antiferromagnetic below 30.8 °K. It has been suggested that there may be a displacement of the uranium ions associated with the magnetic phase transition. X‐ray measurements show that provided the antiferromagnetic domains are sufficiently large (several hundred Å) a possible uranium movement in the 〈100〉 directions is less than 0.0076 Å.