Combining Bayes Classification and Point Group Symmetry under Boolean Framework for Enhanced Protein Quaternary Structure Inference

Our ability to infer the protein quaternary structure automatically from atom and lattice information is inadequate, especially for weak complexes, and heteromeric quaternary structures. Several approaches exist, but they have limited performance. Here, we present a new scheme to infer protein quaternary structure from lattice and protein information, with all-around coverage for strong, weak and very weak affinity homomeric and heteromeric complexes. The scheme combines naive Bayes classifier and point group symmetry under Boolean framework to detect quaternary structures in crystal lattice. It consistently produces >= 90% coverage across diverse benchmarking data sets, including a notably superior 95% coverage for recognition heteromeric complexes, compared with 53% on the same data set by current state-of-the-art method. The detailed study of a limited number of prediction-failed cases offers interesting insights into the intriguing nature of protein contacts in lattice. The findings have implications for accurate inference of quaternary states of proteins, especially weak affinity complexes.

Phase equilibria in the system CaO-CoO-SiO2 and Gibbs energies of formation of the quaternary oxides CaCoSi2O6, Ca2CoSi2O7, and CaCoSiO4

Phase relations in the pseudoternary system CaO-CoO-SiO2 have been established at 1323 K. Three quaternary oxides were found to be stable: CaCoSi2O6 with clinopyroxene (Cpx), Ca2CoSi2O7 with melilite (Mel), and CaCoSiO4 with olivine (Ol) structures. The Gibbs energies of formation of the quaternary oxides from their component binary oxides were measured using solid-state galvanic cells incorporating yttria-stabilized zirconia as the solid electrolyte in the temperature range of 1000-1324 K. The results can be summarized as follows: CoO (rs) + CaO (rs) + 2SiO(2) (Qtz) --> CaCoSi2O6 (Cpx), Delta G(f)(0) = -117920 + 11.26T (+/-150) J/mol CoO (rs) + 2CaO (rs) + 2SiO(2) (Qtz) --> Ca2CoSi2O7 (Mel), Delta G(f)(0) = -192690 + 2.38T (+/-130) J/mol CoO (rs) + CaO (rs) + SiO2 (Qtz) --> CaCoSiO2 (Ol), Delta G(f)(0) = -100325 + 2.55T (+/-100) J/mol where rs = rock salt (NaCl) structure and Qtz = quartz. The uncertainty limits correspond to twice the standard error estimate. The experimentally observed miscibility gaps along the joins CaO-CoO and CaCoSiO4-Co2SiO4 were used to calculate the excess free energies of mixing for the solid solutions CaxCo1-xO and (CayCo1-y)CoSiO4:Delta G(E) = X(1 - X)[31975X + 26736 (1 - X)] J/mol and Delta G(E) = 23100 (+/-250) Y(1 - Y) J/mol. A T-X phase diagram for the binary CaO-CoO was computed from the thermodynamic information; the diagram agrees with information available in the literature. The computed miscibility gap along the CaCoSiO4-Co2SiO4 join is associated with a critical temperature of 1389 (+/-15) K. Stability fields for the various solid solutions and the quaternary compounds are depicted on chemical-potential diagrams for SiO2, CaO, and CoO at 1323 K.

Stereospecific construction of stereogenic vicinal quaternary carbon atoms. Enantiospecific synthesis of (+)-valerane

Stereo- and enantiospecific synthesis of (+)-valerane starting from R-carvone utilising orthoester Claisen rearrangement and intramolecular diazo ketone cyclopropanation reactions for the construction of the two vicinal quaternary carbon atoms is described. Copyright (C) 1996 Elsevier Science Ltd.

Representation of thermodynamic properties of quaternary systems using interaction parameters

Integral excess free energy of a quaternary system has been expressed in terms of the MacLaurin infinite series. The series is subjected to appropriate boundary conditions and each of the derivatives correlated to the corresponding interaction coefficients. The derivation of the partial functions involves extensive summation of various infinite series pertaining to the first order and quaternary parameters to remove any truncational error. The thermodynamic consistency of the derived partials has been established based on the Gibbs-Duhem relations. The equations are used to interpret the thermodynamic properties of the Fe-Cr-Ni-N system.

Profiling of late Tertiary-early Quaternary surface in the lower reaches of Narmada valley using microtremors

In this paper, we propose the first approximation for thickness of Quaternary sediment and late Quaternary early Tertiary topography for the part of lower reaches of Narmada valley in a systematic way using the shallow seismic method, that records both horizontal and vertical components of the microtremor (ambient noise) caused by natural processes. The measurements of microtremors were carried out at 31 sites spaced at a grid interval of 5 km s using Lennartz seismometer (5 s period) and City shark-II data acquisition system. The signals recorded were analysed for horizontal to the vertical (H/V) spectral ratio using GEOPSY software. For the present study, we concentrate on frequency range between 0.2 Hz and 10 Hz. The thickness of unconsolidated sediments at various sites is calculated based on non-linear regression equations proposed by Ibs-von Seht and Wohlenberg (1999) and Parolai et al. (2002). The estimated thickness is used to plot digital elevation model and cross profiles correlating with geomorphology and geology of the study area. (C) 2011 Elsevier Ltd. All rights reserved.

Rearrangement approaches to sesquiterpenes containing multiple contiguous quaternary carbon atoms. Total synthesis of (+/-)-myltayl-8(12)-ene and (+/-)-6-epijunicedranol

Details of the first total syntheses of the sesquiterpenes myltayl-8(12)-ene and 6-epijunicedran-8-ol are described. The aldehyde 13, obtained by Claisen rearrangement of cyclogeraniol, was transformed into the dienones 12 and 18. Boron trifluoride-diethyl ether mediated cyclization and rearrangement transformed the dienones 12 and 18 into the tricyclic ketones 16 and 17, efficiently creating three and four contiguous quaternary carbon atoms, respectively. Wittig methylenation of 16 furnished (+/-)-myltayl-8(12)-ene (11), whereas reduction of the ketone 17 furnished (+/-)-6-epijunicedranol (23).

Thermodynamic modeling of quaternary Al-Ga-In-As system

The present research describes the modeling of the thermodynamic properties of the liquid Al-Ga-In-As alloys at 1073 and 1173 K, and investigates the solid-liquid equilibria in the systems. The isothermal molar excess free energy function for the liquid alloys is represented in terms of 37 parameters pertaining to six of the constituent binaries, four ternaries and the quaternary interactions in the system. The corresponding solid alloys which consist of AlAs, GaAs and InAs are assumed to be quasi-regular ternary solutions. The solidus and liquidus compositions are calculated at 1073 and 1173 K using the derived values of the partial components for the solid and liquid alloys at equilibrium. They are in good agreement with those of the experimentally determined values available in the literature. (C) 1999 Elsevier Science S.A. All rights reserved.

Prediction of activities of oxygen in dilute quaternary solutions using binary data

Equations are developed for predicting the activity coefficients of oxygen dissolved in ternary liquid alloys. These are extensions of earlier treatments, and are based on a model in which each oxygen atom is assumed to make four bonds with neighboring metal atoms. It is also postulated that the strong oxygen-metal bonds distort the electronic configuration around the metal atoms bonded to oxygen, and that the quantitative reduction of the strength of bonds made by these atoms with all of the adjacent metal atoms is equivalent to a factor of approximately two. The predictions of the quasichemical equation which is derived agree satisfactorily with the partial molar free energies of oxygen in Ag-Cu-Sn solutions at 1200°C reported in literature. An extension of this treatment to multicomponent solutions is also indicated.

Computation of thermodynamic properties of quaternary and higher order systems from binary data using shortest distance composition paths

Equations for the computation of integral and partial thermodynamic properties of mixing in quarternary systems are derived using data on constituent binary systems and shortest distance composition paths to the binaries. The composition path from a quarternary composition to the i-j binary is characterized by a constant value of (Xi − Xj). The merits of this composition path over others with constant values for View the MathML source or Xi are discussed. Finally the equations are generalized for higher order systems. They are exact for regular solutions, but may be used in a semiempirical mode for non-regular solutions.

Quaternary association in beta-prism I fold plant lectins: Insights from X-ray crystallography, modelling and molecular dynamics

Dimeric banana lectin and calsepa, tetrameric artocarpin and octameric heltuba are mannose-specific beta-prism I fold lectins of nearly the same tertiary structure. MD simulations on individual subunits and the oligomers provide insights into the changes in the structure brought about in the protomers on oligomerization, including swapping of the N-terminal stretch in one instance. The regions that undergo changes also tend to exhibit dynamic flexibility during MD simulations. The internal symmetries of individual oligomers are substantially retained during the calculations. Energy minimization and simulations were also carried out on models using all possible oligomers by employing the four different protomers. The unique dimerization pattern observed in calsepa could be traced to unique substitutions in a peptide stretch involved in dimerization. The impossibility of a specific mode of oligomerization involving a particular protomer is often expressed in terms of unacceptable steric contacts or dissociation of the oligomer during simulations. The calculations also led to a rationale for the observation of a heltuba tetramer in solution although the lectin exists as an octamer in the crystal, in addition to providing insights into relations among evolution, oligomerization and ligand binding.

Catalytic enantioselective construction of quaternary stereocenters by direct vinylogous Michael addition of deconjugated butenolides to nitroolefins

A direct vinylogous Michael reaction of gamma-substituted deconjugated butenolides with nitroolefins has been developed with the help of a newly identified quinine-derived bifunctional catalyst, allowing the synthesis of densely functionalized products with contiguous quaternary and tertiary stereocenters in excellent yield with perfect diastereoselectivity (>20 : 1 dr) and high enantioselectivity (up to 99 : 1 er).

Catalytic Asymmetric Direct Vinylogous Michael Addition of Deconjugated Butenolides to Maleimides for the Construction of Quaternary Stereogenic Centers

Competition under control: A practical and efficient direct asymmetric vinylogous Michael reaction of deconjugated butenolides has been developed (see scheme). The products of this reaction, highly functionalized chiral succinimides, are obtained in excellent yield with high diastereoselectivity (up to d.r.=18:1) and outstanding enantioselectivity (up to e.r.=99.5:0.5).

Measurement and correlation of quaternary solubilities of dihydroxybenzene isomers in supercritical carbon dioxide

The equilibrium quaternary solubilities of dihydroxybenzene (resorcinol + pyrocatechol + hydroquinone + SCCO2) isomers were experimentally determined at 308, 318 and 328K over a pressure range of 9.8-15.7 MPa by using a saturation method. The effects of temperature, pressure and the components on each other have been thoroughly investigated. The selectivity of SCCO2 for ternary (resorcinol + pyrocatechol + SCCO2) and quaternary systems was discussed. A new model equation for quaternary solubilities of solids has been developed by accounting for non-idealities by combining the solution model with Wilson activity coefficient model. The model equation has five adjustable parameters and correlates the quaternary solubilities of current data along with two other quaternary data reported in the literature. (C) 2012 Elsevier B.V. All rights reserved.

Evidence of an intermediate phase in a quaternary Ag bearing telluride glass system using alternating DSC

Alternating Differential Scanning Calorimetric (ADSC) studies on quaternary Ge15Te80-xIn5Agx glasses show the non-reversing enthalpy (Delta H-NR) at T-g to exhibit a broad global minimum in the 8% <= x <= 16% range of Ag, an observation that is taken evidence for existence of an Intermediate Phase (IP) in that range. Glasses at x < 8% are in the flexible phase while those at x > 16% in the stressed-rigid phase. The nature of crystalline phases formed upon crystallization of bulk glasses are elucidated by XRD studies, and reveal presence of Te, GeTe, Ag8GeTe6, AgTe, In2Te3 and In4Te3 phases. These experiments also reveal that the fraction of Ag- bearing phases increases while those of Te- bearing ones decreases with increasing x, suggesting progressive replacement of Te-Te bonds by Ag-Te bonds. (C) 2013 Elsevier Ltd. All rights reserved.

Raman signatures of intermediate phase in quaternary Ge15Te80 (-) xIn5Agx glasses

Micro-Raman studies are conducted on as-quenched and annealed Ge15Te80 -_xIn5Agx glasses to probe the structural network and its evolution with composition. These studies reveal the presence of tetrahedral GeTe4 structural units in as-quenched samples. Specific signatures of the intermediate phase (IP) are observed in the composition dependence of Raman frequencies and corresponding intensities of different modes in the composition range, 8 <= x <= 16. In addition, the Raman peak positions are found to shift with silver doping. Apart from the Raman results, the compositional dependence of density, molar volume and thermal diffusivity, observed in the present study, confirms the presence of the intermediate phase. In thermally annealed samples, a unique variation of Raman wave-numbers in the intermediate region is observed due to the retention of some of the local structure even after the sample is crystallized. The observed Raman peaks are attributed to crystalline tellurium and silver lattice vibrational modes. Based on our present and earlier studies, we propose the occurrence of three thresholds in Ge15Te80 - xIn5Agx glasses, namely percolation of rigidity, percolation of stress and the onset of chemical phase separation on a nanoscale at 8%, 16% and 20% of silver concentration respectively. (C) 2014 Elsevier B.V. All rights reserved.