Classification of Protein Kinases on the Basis of Both Kinase and Non-Kinase Regions

Background: Protein phosphorylation is a generic way to regulate signal transduction pathways in all kingdoms of life. In many organisms, it is achieved by the large family of Ser/Thr/Tyr protein kinases which are traditionally classified into groups and subfamilies on the basis of the amino acid sequence of their catalytic domains. Many protein kinases are multidomain in nature but the diversity of the accessory domains and their organization are usually not taken into account while classifying kinases into groups or subfamilies. Methodology: Here, we present an approach which considers amino acid sequences of complete gene products, in order to suggest refinements in sets of pre-classified sequences. The strategy is based on alignment-free similarity scores and iterative Area Under the Curve (AUC) computation. Similarity scores are computed by detecting common patterns between two sequences and scoring them using a substitution matrix, with a consistent normalization scheme. This allows us to handle full-length sequences, and implicitly takes into account domain diversity and domain shuffling. We quantitatively validate our approach on a subset of 212 human protein kinases. We then employ it on the complete repertoire of human protein kinases and suggest few qualitative refinements in the subfamily assignment stored in the KinG database, which is based on catalytic domains only. Based on our new measure, we delineate 37 cases of potential hybrid kinases: sequences for which classical classification based entirely on catalytic domains is inconsistent with the full-length similarity scores computed here, which implicitly consider multi-domain nature and regions outside the catalytic kinase domain. We also provide some examples of hybrid kinases of the protozoan parasite Entamoeba histolytica. Conclusions: The implicit consideration of multi-domain architectures is a valuable inclusion to complement other classification schemes. The proposed algorithm may also be employed to classify other families of enzymes with multidomain architecture.

Search on a hypercubic lattice using a quantum random walk. II. d = 2

We investigate the spatial search problem on the two-dimensional square lattice, using the Dirac evolution operator discretized according to the staggered lattice fermion formalism. d = 2 is the critical dimension for the spatial search problem, where infrared divergence of the evolution operator leads to logarithmic factors in the scaling behavior. As a result, the construction used in our accompanying article A. Patel and M. A. Rahaman, Phys. Rev. A 82, 032330 (2010)] provides an O(root N ln N) algorithm, which is not optimal. The scaling behavior can be improved to O(root N ln N) by cleverly controlling the massless Dirac evolution operator by an ancilla qubit, as proposed by Tulsi Phys. Rev. A 78, 012310 (2008)]. We reinterpret the ancilla control as introduction of an effective mass at the marked vertex, and optimize the proportionality constants of the scaling behavior of the algorithm by numerically tuning the parameters.

Electrochemical reduction of Cu(II)-EDTA complex at dropping mercury electrode. An impedance approach

The study of electrochemical reduction of Cu(II)-EDTA system by phase sensitive a.c. impedance method at dropping mercury electrode reveals several interesting features. The complex plane polarograms exhibit loop like shape in contrast to the classical zinc ion reduction where crest like shape is found. Again, the relative placement of peaks of in-phase and quadrature components, and the relative placement of portions before and after the peaks of complex plane polarograms are different from that of zinc ion reduction. The complex plane plots suggest that electrochemical reduction of Cu-EDTA is charge transfer controlled.

Electrophilic Substitution Reactions of Copper(II) Acetylacetoneimine Complexes with Arene Diazonium Ions

Copper(II) complexes of ethylene/propylene-bis(acetylacetoneimine), Cu(baen) or Cu(bapn), react quickly and quantitatively in aqueous methanol at the methine position with arene diazonium ions in a stepwise manner to yield mono- and di-substituted copper(II) complexes. All the complexes are paramagnetic with μeff∼1.88 B.M. In all the complexes the diazo substituted part of the ligand coordinates to the metal through the agr-nitrogen of the azo group and the imine nitrogen, forming glyoxaliminearylhydrazone type of ligand system. The complexes have been characterized by elemental analysis, electronic, esr, ir and mass spectroscopic methods.

Correlation of helicopter rotor aeroelastic response with HART-II wind tunnel test data

Purpose - This paper aims to validate a comprehensive aeroelastic analysis for a helicopter rotor with the higher harmonic control aeroacoustic rotor test (HART-II) wind tunnel test data. Design/methodology/approach - Aeroelastic analysis of helicopter rotor with elastic blades based on finite element method in space and time and capable of considering higher harmonic control inputs is carried out. Moderate deflection and coriolis nonlinearities are included in the analysis. The rotor aerodynamics are represented using free wake and unsteady aerodynamic models. Findings - Good correlation between analysis and HART-II wind tunnel test data is obtained for blade natural frequencies across a range of rotating speeds. The basic physics of the blade mode shapes are also well captured. In particular, the fundamental flap, lag and torsion modes compare very well. The blade response compares well with HART-II result and other high-fidelity aeroelastic code predictions for flap and torsion mode. For the lead-lag response, the present analysis prediction is somewhat better than other aeroelastic analyses. Research limitations/implications - Predicted blade response trend with higher harmonic pitch control agreed well with the wind tunnel test data, but usually contained a constant offset in the mean values of lead-lag and elastic torsion response. Improvements in the modeling of the aerodynamic environment around the rotor can help reduce this gap between the experimental and numerical results. Practical implications - Correlation of predicted aeroelastic response with wind tunnel test data is a vital step towards validating any helicopter aeroelastic analysis. Such efforts lend confidence in using the numerical analysis to understand the actual physical behavior of the helicopter system. Also, validated numerical analyses can take the place of time-consuming and expensive wind tunnel tests during the initial stage of the design process. Originality/value - While the basic physics appears to be well captured by the aeroelastic analysis, there is need for improvement in the aerodynamic modeling which appears to be the source of the gap between numerical predictions and HART-II wind tunnel experiments.

Characterization of hot deformation behavior of brasses using processing maps: Part II. β Brass and α-β brass

The hot deformation behaviors of β brass in the temperature range of 550°C to 800°C and α-β brass in the temperature range of 450°C to 800°C have been characterized in the strain rate range of 0.001 to 100 s−1 using processing maps developed on the basis of the Dynamic Materials Model. The map for β brass revealed a domain of superplasticity in the entire temperature range and at strain rates lower than 1 s−1, with a maximum efficiency of power dissipation of about 68 pct. The temperature variation of the efficiency of power dissipation in the domain is similar to that of the diffusion coefficient for zinc in β brass, confirming that the diffusion-accommodated flow controls the superplasticity. The material undergoes microstructural instability in the form of adiabatic shear bands and strain markings at temperatures lower than 700°C and at strain rates higher than 10 s−1. The map for α-β brass revealed a wide domain for processing in the temperature range of 550°C to 800°C and at strain rates lower than 1 s−1, with a maximum efficiency of 54 pct occurring at about 750°C and 0.001 s−1. In the domain, the α phase undergoes dynamic recrystallization and controls the hot deformation of the alloy, while the β phase deforms superplastically. At strain rates greater than 1 s−1, α-β brass exhibits microstructural instabilities manifested as flow rotations at lower temperatures and localized shear bands at higher temperatures.

Mammalian Mat1 subunit of Transcription Factor IIH in gene-specific and general transcription

All protein-encoding genes in eukaryotes are transcribed into messenger RNA (mRNA) by RNA Polymerase II (RNAP II), whose activity therefore needs to be tightly controlled. An important and only partially understood level of regulation is the multiple phosphorylations of RNAP II large subunit C-terminal domain (CTD). Sequential phosphorylations regulate transcription initiation and elongation, and recruit factors involved in co-transcriptional processing of mRNA. Based largely on studies in yeast models and in vitro, the kinase activity responsible for the phosphorylation of the serine-5 (Ser5) residues of RNAP II CTD has been attributed to the Mat1/Cdk7/CycH trimer as part of Transcription Factor IIH. However, due to the lack of good mammalian genetic models, the roles of both RNAP II Ser5 phosphorylation as well as TFIIH kinase in transcription have provided ambiguous results and the in vivo kinase of Ser5 has remained elusive. The primary objective of this study was to elucidate the role of mammalian TFIIH, and specifically the Mat1 subunit in CTD phosphorylation and general RNAP II-mediated transcription. The approach utilized the Cre-LoxP system to conditionally delete murine Mat1 in cardiomyocytes and hepatocytes in vivo and and in cell culture models. The results identify the TFIIH kinase as the major mammalian Ser5 kinase and demonstrate its requirement for general transcription, noted by the use of nascent mRNA labeling. Also a role for Mat1 in regulating general mRNA turnover was identified, providing a possible rationale for earlier negative findings. A secondary objective was to identify potential gene- and tissue-specific roles of Mat1 and the TFIIH kinase through the use of tissue-specific Mat1 deletion. Mat1 was found to be required for the transcriptional function of PGC-1 in cardiomyocytes. Transriptional activation of lipogenic SREBP1 target genes following Mat1 deletion in hepatocytes revealed a repressive role for Mat1apparently mediated via co-repressor DMAP1 and the DNA methyltransferase Dnmt1. Finally, Mat1 and Cdk7 were also identified as a negative regulators of adipocyte differentiation through the inhibitory phosphorylation of Peroxisome proliferator-activated receptor (PPAR) γ. Together, these results demonstrate gene- and tissue-specific roles for the Mat1 subunit of TFIIH and open up new therapeutic possibilities in the treatment of diseases such as type II diabetes, hepatosteatosis and obesity.

Diastereoisomeric (η6-arene)ruthenium(II) chiral Schiff base complexes: crystal structure of a triphenylphosphine adduct

Reaction of [(eta-6-p-cymene)RuCl(L star)] with AgClO4 in Me2CO gives a perchlorate complex which on subsequent treatment with PPh3, gamma-picoline or Cl- yields adducts showing that there can be retention as well as inversion of configuration at the metal centre. The (R)Ru,(S)C absolute configurations of the chiral centres in the triphenylphosphine adduct have been established by an X-ray diffraction study [HL star, (S)-alpha-methylbenzylsalicylaldimine]. The CD spectral study reveals that there is an inversion of configuration during formation of the PPh3 adduct.

Theoretical gain‐optimization studies in CO2–N2 gasdynamic lasers. II. Results of parametric study

Based on a method presented in detail in a previous work by the authors, similar solutions have been obtained for the steady inviscid quasi‐one‐dimensional nonreacting flow in the supersonic nozzle of a CO2–N2 gasdynamic laser system, with either H2O or He as the catalyst. It has been demonstrated how these solutions could be used to optimize the small‐signal gain coefficient on a specified vibrational‐rotational transition. Results presented for a wide range of mixture compositions include optimum values for the small‐signal gain, area ratio, reservoir temperature, and a binary scaling parameter, which is the product of reservoir pressure and nozzle shape factor.

Immediate hypersensitivity to Parthenium hysterophorus. II. Clinical studies on the prevalence of parthenium rhinitis

The airborne pollen of the South American weed, Parthenium hysterophorus (American feverfew), accidentally introduced into India was found to be responsible for severe allergic rhinitis. A random clinical survey conducted on 2035 residents of Bangalore city with the aid of questionnaires and skin tests revealed that 7.1% of the study population was suffering from allergic rhinitis due to exposure to Parthenium pollen. Skin-prick tests performed on 1294 clinic patients suffering from nasobronchial allergy during the past 4 years have also shown that 42.5% were sensitive to Parthenium pollen. IgE and IgG antibodies specific for Parthenium pollen allergens were demonstrable in the sera of Parthenium-sensitive rhinitis patients. The specificity of these antibodies to Parthenium allergens was established by ELISA. A 7- to 11-fold higher stimulation was observed when lymphocytes from two Parthenium-sensitive rhinitis patients were treated in vitro with Parthenium pollen extract. To our knowledge, nowhere in the world has such a high incidence of allergic rhinitis due to a single pollen ever been reported.

Studies in biogas technology. Part II. Optimisation of plant dimensions

In this paper, the design basis of the conventional Khadi and Village Industries Commission biogas plants has been elucidated. It has been shown that minimisation of the cost of the gas holder alone leads to the narrow and deep digesters of conventional plants. If instead, the total capital cost of the gas holder plus digester is minimised, the optimisation leads to wide and shallow digesters, which are less expensive. To test this alternative, two prototype plants have been designed, constructed and operated. These plants are not only 25–40% cheaper, but their performance is actually slightly better than the conventional plants.

New chelating resins based on polybenzimidazole. Selective sorption of copper(II) from ammoniacal media on resin with anchored l-cysteine

Microporous polybenzimidazole (PBI) of 250–500 μm bead size has been epoxidized and subsequently reacted with l-cysteine in the presence of a phase-transfer catalyst at room temperature to obtain a sorbent having anchored l-cysteine, EPBI(Cyst). The sorption of Cu(II), Ni(II), Co(II), and Zn(II) in mildly acidic and ammoniacal solutions has been measured under comparable conditions on EPBI(Cyst) and Dowex 50W-X8(H+) resins. While the latter shows no appreciable difference in sorption of the four metals in acidic and ammoniacal media and has 40–60 % selectivity for copper(II) over the other three, EPBI(Cyst) shows a threefold increase in copper sorption and more than 90% copper selectivity over the other metals in ammoniacal media, compared to mildly acidic media. The copper binding constant and saturation capacity of EPBI(Cyst) in ammoniacal media decrease only slowly beyond pH 11.6 with the result that the resin shows significant sorption of Cu(II) even in strongly ammoniacal solutions. The sorbed copper is stripped with HCl relatively easily. The copper sorption kinetics on EPBI(Cyst) is unusually fast in ammoniacal media with more than 90 % of equilibrium sorption being attained in one minute.