Docking and free energy simulations to predict conformational domains involved in hCG-LH receptor interactions using recombinant antibodies

Single chain fragment variables (ScFvs) have been extensively employed in studying the protein-protein interactions. ScFvs derived from phage display libraries have an additional advantage of being generated against a native antigen, circumventing loss of information on conformational epitopes. In the present study, an attempt has been made to elucidate human chorionic gonadotropin (hCG)-luteinizing hormone (LH) receptor interactions by using a neutral and two inhibitory ScFvs against hCG. The objective was to dock a computationally derived model of these ScFvs onto the crystal structure of hCG and understand the differential roles of the mapped epitopes in hCG-LH receptor interactions. An anti-hCG ScFv, whose epitope was mapped previously using biochemical tools, served as the positive control for assessing the quality of docking analysis. To evaluate the role of specific side chains at the hCG-ScFv interface, binding free energy as well as residue interaction energies of complexes in solution were calculated using molecular mechanics Poisson-Boltzmann/surface area method after performing the molecular dynamic simulations on the selected hCG-ScFv models and validated using biochemical and SPR analysis. The robustness of these calculations was demonstrated by comparing the theoretically determined binding energies with the experimentally obtained kinetic parameters for hCG-ScFv complexes. Superimposition of hCG-ScFv model onto a model of hCG complexed with the 51-266 residues of LH receptor revealed importance of the residues previously thought to be unimportant for hormone binding and response. This analysis provides an alternate tool for understanding the structure-function analysis of ligand-receptor interactions. Proteins 2011;79:3108-3122. (C) 2011 Wiley-Liss, Inc.

Effect of pairing fluctuations on low-energy electronic spectra in cuprate superconductors

We describe here a minimal theory of tight-binding electrons moving on the square planar Cu lattice of the hole-doped cuprates and mixed quantum mechanically with their own Cooper pairs. The superconductivity occurring at the transition temperature T(c) is the long-range, d-wave symmetry phase coherence of these Cooper pairs. Fluctuations, necessarily associated with incipient long-range superconducting order, have a generic large-distance behavior near T(c). We calculate the spectral density of electrons coupled to such Cooper-pair fluctuations and show that features observed in angle resolved photoemission spectroscopy (ARPES) experiments on different cuprates above T(c) as a function of doping and temperature emerge naturally in this description. These include ``Fermi arcs'' with temperature-dependent length and an antinodal pseudogap, which fills up linearly as the temperature increases toward the pseudogap temperature. Our results agree quantitatively with experiment. Below T(c), the effects of nonzero superfluid density and thermal fluctuations are calculated and compared successfully with some recent ARPES experiments, especially the observed bending or deviation of the superconducting gap from the canonical d-wave form.

Vapor pressure and dissociation energy of (In2O)

The vapor pressure of pure liquid indium, and the sum of pressures of (In) and (In2O) species over the condensed phase mixture {In} + , contained in a silica vessel, have been measured by Knudsen effusion and Langmuir free vaporization methods in the temperatue range 600 to 950°C. Mass spectrometric studies reported in the literature show that (In) and (In2O) are the important species in the vapor phase over the {In} + ; mixture. The vapor pressure of (In2O) corresponding to the reaction, deduced from the present measurements is given by the equation, The “apparent evaporation coefficient” for the condensed phase mixture is approximately 0.8. The energy for the dissociation (In2O) molecule into atoms calculated from the above equation is D°0 = 180.0 (± 1.0) kcal mol−1.

Potentiometric determination of the Gibbs free energy of formation of cadmium and magnesium chromites

The standard Gibbs free energy of formation of magnesium and cadmiumchromites have been determined by potentiometric measurements on reversiblesolid-state electrochemical cells [dformula (Au-5%Cd, , Au-5%Cd; Pt, + , CaO-ZrO[sub 2], + ,Pt; CdO, , CdCr[sub 2]O[sub 4] + Cr[sub 2]O[sub 3])] in the temperature range 500°–730°C, and [dformula Pt, Cr + Cr[sub 2]O[sub 3]/Y[sub 2]O[sub 3]-ThO[sub 2]/Cr + MgCr[sub 2]O[sub 4] + MgO, Pt] in the temperature range 800°–1200°C. The temperature dependence of the freeenergies of formation of the ternary compounds can be represented by theequations [dformula CdO(r.s.) + Cr[sub 2]O[sub 3](cor) --> CdCr[sub 2]O[sub 4](sp)] [dformula Delta G[sup 0] = - 42,260 + 7.53T ([plus-minus]400) J] and [dformula MgO(r.s.) + Cr[sub 2]O[sub 3](cor) --> MgCr[sub 2]O[sub 4](sp)] [dformula Delta G[sup 0] = - 45,200 + 5.36T ([plus-minus]400) J] The entropies of formation of these spinels are discussed in terms of cationdisorder and extent of reduction of Cr3+ ions to Cr2+ ions. Thermodynamicdata on the chromates of cadmium and magnesium are derived by combiningthe results obtained in this study with information available in the literatureon high temperature, high pressure phase equilibria in the systems CdO-Cr2O3-O2 and MgO-Cr2O3-O2.

Gibbs free energy of formation of magnesium stannate

he thermodynamic properties of the spinel Mg2SnO4 have been determined by emf measurements on the solid oxide galvanic cell,View the MathML source in the temperature range 600 to 1000°C. The Gibbs' free energy of formation of Mg2SnO4 from the component oxides can be expressed as View the MathML source,View the MathML source These values are in good agreement with the information obtained by Jackson et al. [Earth Planet. Sci. Lett.24, 203 (1974)] on the high pressure decomposition of magnesium stannate into component oxides at different temperatures. The thermodynamic data suggest that the spinel phase is entropy stabilized, and would be unstable below 207 (±25)°C at atmospheric pressure. Based on the information obtained in this study and trends in the stability of aluminate and chromite spinels, it can be deduced that the stannates of nickel and copper(II) are unstable.

Gibbs energy of formation of lead zirconate

The Gibbs energy of formation of zirconia-saturated lead zirconate was determined by emf measurements on the solid state cells and at 800 to 1400 K. The results obtained differ significantly from those reported in the literature based on vapor-pressure measurements, using Knudsen effusion and transportation techniques and assuming that the vapor phase consisted entirely of monomeric PbO molecules. A reanalysis of the data obtained in the earlier vapor-pressure studies, using mass-spectrometric measurements on polymeric PbO species in the gas phase, gives Gibbs energies of formation of lead zirconate which are in better agreement with those obtained in this study. Recent electrochemical measurements using CaO-ZrO2 and PbF2 solid electrolytes are in good agreement with the present study. The results obtained in this study are also consistent with the phase diagram which shows decomposition of the zirconate to tetragonal zirconia and a liquid phase rich in PbO at 1843 K.

Gibbs energy formation of lead titanate

The Gibbs energy of formation of titania-saturated lead titanate has been determined by e.m.f. measurements on the solid state cell;Pt,Ir,Pb + Pb1−xTiO3−x + TiO2(rutile)/CaO-ZrO2/Ni + NiO,Pt in the temperature range 1075–1350 K. The results obtained are significantly different from those reported in the literature based upon vapour pressure measurements, employing Knudsen effusion and transportation techniques, and assuming that the vapor phase consisted entirely of monomeric PbO molecules. A reanalysis of the data obtained in the earlier vapor pressure studies using mass spectrometric measurements on polymeric PbO species in the gas phase, gives Gibbs energies of formation of lead titanate which are in better agreement with those obtained in this study. Earlier electrochemical measurements by Mehrotra et al. and more recent electrochemical measurements by Schmahl et al. both employing CaO-ZrO2 solid electrolytes are in good agreement with the present study. The electro-chemical measurements by Schmahl et al. using PbF 2 solid electrolyte give a slightly more positive Gibbs energy of formation. There was no evidence supporting the formation of compounds other than Pb1−xTiO3−x from yellow PbO and rutile form of TiO2 in the temperature range covered in this study.Résumé L'enthalpie libre de formation du titanate de plomb saturé en oxyde de titane a été déterminée par des mesures de FEM de la pile: Pt,Ir,Pb + Pb1−xTiO3−x + TiO2(rutile)/CaO-ZrO2/Ni + NiO,Pt dans le domaine de températures 1075–1350 K. Les résultats obtenus, different appréciablement de ceux publiés, déterminés par mesures de tensions de vapeur (techniques de transport et d'effusion de Knudsen) en supposant que la phase gazeuse etait uniquement constituée de molécules monomériques de PbO. Une réanalyse des résultats de la littérature, à partir de mesures par spectrométrie de masse sur les polymères de PbO gazeux, donne des enthalpies libres de formation du titanate de plomb se rapprochant de celles obtenues dans cette étude. Les mesures de Mehrotra et al. et plus récemment de Schmahl et al. utilisant toutes deux l'électrolyte CaO-ZrO2 concordent bien avec celles de la présente étude. Les mesures de Schmahl et al., à l'aide de l' électrolyte solide PbF2, donnent une enthalpie de formation légèrement plus positive. Pour la gammede températures étudiée, rien ne permet de supposer que des composés autres que Pb1−x TiO3−x puissent se former à partir du PbO Gaune) et du rutile (TiO2).

Gibbs energy of formation of nickel orthosilicate (Ni2SiO4)

Two solid state galvanic cells:Pt, Ni + Ni2Si04 + Si02/(Y203)Zr02/Ni + + NiO, Pt (1) and Pt, Ni + NizSiOj + Si02/CaF2/Ni + + NiO, Pt (11) have been employed for the determination of the Gibbs' energy of formation of nickel orthosilicate(Ni2Si04) from nickel oxide and quartz. The emf of cell (I) was reversible and reproducible in the temperature range 925 to 1375K whereas emf of cell (11) drifted with time and changed polarity. From the results of cell (I), the Gibbs' energy of formation of nickel silicate is obtained as,2Ni0 (r.s.) + Si02 (quartz) + Ni2Si04 (olivine)Gibbs' energy of formation of the spinel form of Ni2Si04 is obtained by combining the data for olivine obtained in this study with high pressure data on olivine to spinel transition reported in the literature. The complex time dependence of the emf of cell (11) can be rationalised on the basis of formation of calcium silicates from calcium oxide, generally present as an impurity in the calcium fluoride electrolyte, and silica. The emf of cell (11) is shown to be the function of the activity of calcium oxide at the electrolyte/ electrode interface. The results provide strong evidence against the recent suggestion of mixed anionic conduction in calcium fluoride.

The standard molar Gibbs energy of formation of YbPt3 and LuPt3 intermetallics

The standard molar Gibbs energies of formation of YbPt3 and LuPt3 intermetallic compounds have been measured in the temperature range 880 K to 1100 K using the solid-state cells:View the MathML source and View the MathML source The trifluoride of Yb is not stable in equilibrium with Yb or YbPt3. The results can be expressed by the equations: View the MathML source View the MathML source The standard molar Gibbs energy of formation of LuPt3 is −41.1 kJ · mol−1 more negative than that for YbPt3 at 1000 K. Ytterbium is divalent in the pure metal and trivalent in the intermetallic YbPt3. The energy required for the promotion of divalent Yb to the trivalent state is responsible for the less negative ΔfGmo of YbPt3. The enthalpies of formation of the two intermetallics are in reasonable agreement with Miedema's model. Because of the extraordinary stability of these compounds it is possible to reduce oxides of Yb and Lu with hydrogen in the presence of platinum at View the MathML source. The equilibrium chemical potential of oxygen corresponding to the reduction of Yb2O3 and Lu2O3 by hydrogen in the presence of platinum is presented in the form of an Ellingham diagram.

Measurement of the Gibbs energy of formation of URh3 using an oxide solid electrolyte

The Gibbs' energy offormation of the intermetallic compound URh3has been measured in the temperature range 980 to 1320 K using an oxide solid state cell incorporating yttria-doped thoria as the solid electrolyte and a mixture of manganese and manganese oxide as the reference electrode. The cell can be represented as Pt, Mn + MnO I (Y203)Th02 I Rh + URh3 + U02 + x' Rh, Pt The reversible emf of the cell was a linear function of temperature E = 15.60 +0.0237 T (±0.8) mY. Using auxiliary thermodynamic data for MnO and U02+ x the Gibbs' energy of formation of URh3 from component metals has been computed. The results can be expressed by the equation L'.G?< URh3 > = -316240 + 13.22 T (± 3000) J mol-1. The "third-law" enthalpy of formation of URh3at 298 K is -293.2 (± 4) kJ mol-1, significantly more negative than the value of -181.5 kJ mol-1 calculated using Miedema's model.

Gibbs’ energy of formation of YBa2Cu3O7-x (tetragonal)

The high temperature ceramic oxide superconductor YBa2Cu3O7-x (1–2–3 compound) is generally synthesized in an oxygen-rich environment. Hence any method for determining its thermodynamic stability should operate at a high oxygen partial pressure. A solid-state cell incorporating CaF2 as the electrolyte and functioning under pure oxygen at a pressure of 1·01 × 105 Pa has been employed for the determination of the Gibbs’ energy of formation of the 1–2–3 compound. The configuration of the galvanic cell can be represented by: Pt, O2, YBa2Cu3O7−x , Y2BaCuO5, CuO, BaF2/CaF2/BaF2, BaZrO3, ZrO2, O2, Pt. Using the values of the standard Gibbs’ energy of formation of the compounds BaZrO3 and Y2BaCuO5 from the literature, the Gibbs’ energy of formation of the 1–2–3 compound from the constituent binary oxides has been computed at different temperatures. The value ofx at each temperature is determined by the oxygen partial pressure. At 1023 K for O content of 6·5 the Gibbs’ energy of formation of the 1–2–3 compound is −261·7 kJ mol−1.

Gibbs energy of formation of CuCrO4 and phase relations in the system Cu-Cr-O below 735 K

A solid state galvanic cell incorporating yttria-stabilized zirconia electrolyte and ruthenium(IV) oxide electrodes has been used to measure the equilibrium chemical potential of oxygen corresponding to the decomposition of CuCrO4 in the range 590–760 K. For the reaction CuO(tenorite) + CuCr2O4(spinel) + 1.5O2(g)→2CuCrO4(orth), ΔGXXX = −183540 + 249.6T(±900) J mol−1. The decomposition temperature of CuCrO4 in pure oxygen at a pressure of 1.01 × 105 Pa is 735(±1) K. By combining the results obtained in this study with data on the Gibbs energy of formation of CuCr2O4 and CuCrO2 reported earlier, the standard Gibbs energy of formation of CuCrO4 and the phase relations in the system Cu-Cr-O at temperatures below 735 K have been deduced. Electron microscopic studies have indicated that the decomposition of CuCrO4 to CuCr2O4 is topotactic.

Phase equilibria in the system NiO-CaO-SiO2 and Gibbs energy of formation of CaNiSi2O6

Phase relations in the pseudoternary system NiO-CaO-SiO2 at 1373 K are established. The coexisting phases are identified by X-ray diffraction and energy-dispersive X-ray analysis of equilibrated samples. There is only one quaternary oxide CaNiSi2O6 with clinopyroxene structure. The Gibbs energy of formation of CaNiSi2O6 is measured using a solid state galvanic cell incorporating stabilized zirconia as the solid electrolyte in the temperature range of 1000 to 1400 K:Pt, Ni + SiO2 + CaSiO3 + CaNiSi2O6 \ (Y2O3)ZrO2 \ Ni + NiO, Pt From the electromotive force (emf) of the cell, the Gibbs energy of formation of CaNiSi2O6 from NiO, SiO2, and CaSiO3 is obtained. To derive the Gibbs energy of formation of the quaternary oxide from component binary oxides, the free energy of formation of CaSiO, is determined separately using a solid state cell based on single crystal CaF2 as the electrolyte: Pt, O-2, CaO + CaF2 \ CaF2 \ CaSiO3 + SiO2 + CaF2, O-2, Pt The results can be expressed by the following equations: NiO (r.s) + CaO (r.s) + 2SiO(2) (qz) --> CaNiSi2O6 (pyr) Delta G degrees = -115,700 + 10.63T (+/-100) J mol(-1) CaO (r.s) + SiO2 (qz) --> CaSiO3 (wol) Delta G degrees = -90,030 -0.61T (+/-60) J mol(-1).