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.

Wear behavior of plasma electrolytic oxidation (PEO) and hybrid coatings of PEO and laser on MRI 230D magnesium alloy

Wear resistant coatings were produced on a permanent mould cast MRI 230D Mg alloy by (a) PEO in silicate based electrolyte, (b) PEO in phosphate based electrolyte, (c) hybrid coatings of silicate PEO followed by laser surface alloying (LSA) with Al and Al(2)O(3), and (d) hybrid coatings of phosphate PEO followed by LSA with Al and Al(2)O(3). Microstructural characterization of the coatings was carried out by scanning electron microscopy (SEM) and X(ray diffraction. The tribological behavior of the coatings was investigated under dry sliding condition using linearly reciprocating ball-on-flat wear test. Both the PEO coatings exhibited a friction coefficient of about 0.8 and hybrid coatings exhibited a value of about 0.5 against the AISI 52100 steel ball as the friction partner, which were slightly reduced with the increase in applied load. The PEO coatings sustained the test without failure at 2 N load but failed at 5 N load due to micro-fracture caused by high contact stresses. The hybrid coatings did not get completely worn off at 2 N load but were completely removed exposing the substrate at 5 N load. The PEO coatings exhibited better wear resistance than the hybrid coatings and silicate PEO coatings exhibited better wear resistance than the phosphate PEO coatings. Both the PEO coatings melted/decomposed on laser irradiation and all the hybrid coatings exhibited similar microstructure and wear behavior irrespective of the nature of the primary PEO coating or laser energies. SEM examination of worn surfaces indicated abrasive wear combined with adhesive wear for all the specimens. The surface of the ball exhibited a discontinuous transfer layer after the wear test. (C) 2011 Elsevier B.V. All rights reserved.

Activities of oxygen and lead in Pb-Ag O solutions

The reversible e.m.f. of galvanic cells: stainlesssteel,Ir,Pb+PbO|CaO+ZrO2|Ag+Pb+PbO,Ir,stainlesssteel,I and Pt,Ni+NiO|CaO+ZrO2|O(Pb+Ag),Cermet,Pt,II incorporating solid oxide electrolytes were measured as a function of alloy composition. In lead-rich alloys, the temperature dependence of the e.m.f. of cell I was also investigated. Since the solubility of oxygen in the alloy is small, the relative partial molar properties of lead in the binary Ag + Pb system can be calculated from the e.m.f. of this cell. The Gibbs free energies obtained in this study are combined with selected calorimetric data to provide a complete thermodynamic discription of liquid Ag + Pb Alloys. The activity coefficient of oxygen in the whole range of Ag + Pb alloys at 1273 K have been obtained from the e.m.f. of cell II; and these are found to deviate positively from Alcock and Richardson's quasichemical equation when the average co-ordination number of all the atoms is assigned a value of 2.

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.

An improved method for calculating activities from distribution equilibria

The method of Gibbs-Duhem integration suggested by Speiser et al. has been modified to derive activities from distribution equilibria. It is shown that, in general, the activities of components in melts with a common anion can be calculated, without using their standard Gibbs energies of formation, from eqUilibrium ratios and the knowledge of activities in the metal phase. Moreover, if systems are so chosen that the concentration of one element in the metal phase lies in the Henry's law region (less than 1 %), information on activities in the metal phase is not required. Conversely, activities of elements in an alloy can be readily calculated from equilibrium distribution ratios alone, if the salt phase in equilibrium contains very small amounts of one element. Application of the method is illustrated using distribution ratios from the literature on AgCI-CuCI, AgBr-CuBr, and CuDo.5 -PbD systems. The results indicate that covalent bonding and van der Waals repulsive interactions in certain types of fused salt melts can significantly affect the thermodynamic properties of mixing.

Activities of indium in solid solutions of Cu+In, Au+In and Cu+Au+In alloys

Thin foils of Cu, Au and Cu + Au alloys embedded in indium sesquioxide were equilibrated with controlled streams of CO-CO2 mixtures. The equilibrium concentrations of indium in the foils were determined by neutron activation analysis. The corresponding chemical potentials of indium were calculated from the standard free energies of formation of carbon monoxide, carbon dioxide, and indium oxide. It was found that the size difference between the solute and the solvent does not make significant contributions to the solute—solute interaction energy in the α-phase. The chemical potential of indium at one at.% concentration is 8.6 Kcals more negative in gold than in copper at 900°K. The variation of this chemical potential with alloy composition in Cu + Au system was in good agreement with Alcock and Richardson's quasichemical equation. The agreement is strengthened by the accurate knowledge of the co-ordination number in these substitutional solid solutions from X-ray diffraction studies.

Chemical potential of germanium in its solid solutions with Cu, Ag and Au

Thin foils of copper, silver and gold were equilibrated with tetragonal GeO2 under controlled View the MathML source gas streams at 1000 K. The equilibrium concentration of germanium in the foils was determined by the X-ray fluorescence technique. The standard free energy of formation of tetragonal GeO2 was measured by a solid oxide galvanic cell. The chemical potential of germanium calculated from the experimental data and the free energies of formation of carbon monoxide and carbon dioxide was found to decrease in the sequence Ag + Ge > Au + Ge > Cu + Ge. The more negative value for the chemical potential of germanium in solid copper, compared to that in solid gold, cannot be explained in terms of the strain energy factor, electro-negativity differences or the vaporization energies of the solvent, and suggests that the d band and its hybridization with s electrons are an important factor in determining the absolute values for the chemical potential in dilute solutions. However, the variation of the chemical potential with solute concentration can be correlated to the concentration of s and p electrons in the outer shell.

Solute solute and solvent solute interactions in solid solutions of Cu+Sn, Au+Sn and Cu+Au+Sn alloys

The chemical potentials of tin in its α-solid solutions with Cu, Au and Cu + Au alloys have been measured using a gas-solid equilibration technique. The variation of the excess chemical potential of tin with its composition in the alloy is related to the solute-solute repulsive interaction, while the excess chemical potential at infinite dilution of the solute is a measure of solvent-solute interaction energies. It is shown that solute-solute interaction is primarily determined by the concentration of (s + p) electrons in the conduction band, although the interaction energies are smaller than those predicted by either the rigid band model or calculation based on Friedel oscillations in the potential function. Finally, the variation of the solvent-solute interaction with solvent composition in the ternary system can be accounted for in terms of a quasi-chemical treatment which takes into account the clustering of the solvent atoms around the solute.

Thermodynamics of CuAlO2 and CuAl2O4 and phase equilibria in the system Cu2O CuO-Al2O3

The standard Gibbs free energies of formation of CuAlO2 and CuAl2O4 were determined in the range 700° to 1100°C, using emf measurements on the galvanic cells (1) Pt,CuO +] Cu2O/CaO-ZrO2/O2,Pt; (2) Pt,Cu +] CuAlO2+] Al2O3/CaO-ZrO2/ Cu +] Cu2O,Pt; and (3) Pt,CuAl2O4+] CuAlO2+]Al2O3/CaO-ZrO2/O2,Pt. The results are compared with published information on the stability of these compounds. The entropy of transformation of CuO from tenorite to the rock-salt structure is evaluated from the present results and from earlier studies on the entropy of formation of spinels from oxides of the rock-salt and corundum structures. The temperatures corresponding to 3-phase equilibria in the system Cu2O-CuO-Al2O3 at specified O2 pressures calculated from the present results are discussed in reference to available phase diagrams.

Evidence of residual entropy in the cubic spinel Zn2TiO4

The standard free energies of formation of Zn2Ti04 and ZnTi03 have been determined in the temperature range 930° to i ioo'x from electromotive force measurements on reversible solid oxide galvanic cells;Ag-5at%znll I Pt, + CaO-Zr02 ZnO I II Ag-5at%Zn Y20r Th02 CaO-Zr02 + ,Pt Zn2Ti04+ ZnTi03 and II Ag-5at%Zn CaO-Zr02 + ,Pt ZnTi03+ Ti02 The values may be expressed by the equations,2ZnO (wurtz) + Ti02(rut) -> Zn2Ti04(sp), f:!:.Go = -750-2-46T (±75)cal;ZnO(wurtz) +Ti02(rut) -> ZnTi03(ilmen) ,f:!:.Co = -]600-0·]99T(±50)cal.Combination of the free energy values with the calorimetric heat of formation, and low-temperature and high-temperature heat capacity of Zn2Ti04 reported in literature, suggests a residual entropy of ],9 (±0·6) cal K-1 mol ? for the cubic spinel. Ideal mixing of Zn2+ and Ti4+ ions on the octahedral sites would result in a configurational contribution to the entropy of 2· 75 cal K-1 rnol ".The difference is indicative of short-range ordering of cations on octahedral sites.

Thermodynamics and phase equilibria in the system Cu2O CuO ()Ga2O3

The standard Gibbs free energies of formation of CuAlO2 and CuAl2O4 were determined in the range 700° to 1100°C, using emf measurements on the galvanic cells (1) Pt,CuO +] Cu2O/CaO-ZrO2/O2,Pt; (2) Pt,Cu +] CuAlO2+] Al2O3/CaO-ZrO2/ Cu +] Cu2O,Pt; and (3) Pt,CuAl2O4+] CuAlO2+]Al2O3/CaO-ZrO2/O2,Pt. The results are compared with published information on the stability of these compounds. The entropy of transformation of CuO from tenorite to the rock-salt structure is evaluated from the present results and from earlier studies on the entropy of formation of spinels from oxides of the rock-salt and corundum structures. The temperatures corresponding to 3-phase equilibria in the system Cu2O-CuO-Al2O3 at specified O2 pressures calculated from the present results are discussed in reference to available phase diagrams.

Solubility and activity of oxygen in liquid gallium and gallium copper alloys

The solubility of oxygen in liquid gallium in the temperature range 775 –1125 °C and in liquid gallium-copper alloys at 1100 °C, in equilibrium with β-Ga2O3, has been measured by an isopiestic equilibrium technique. The solubility of oxygen in pure gallium is given by the equation log (at.% O) = −7380/T + 4.264 (±0.03) Using recently measured values for the standard free energy of formation of β-Ga2O3 and assuming that oxygen obeys Sievert's law up to the saturation limit, the standard free energy of solution of oxygen in liquid gallium may be calculated : View the MathML sourceΔ°298 = −52 680 + 6.53T (±200) cal where the standard state for dissolved oxygen is an infinitely dilute solution in which the activity is equal to atomic per cent. The effect of copper on the activity of oxygen dissolved in liquid gallium is found to be in good agreement with that predicted by a recent quasichemical model in which it was assumed that each oxygen is interstitially coordinated to four metal atoms and that the nearest neighbour metal atoms lose approximately half their metallic cohesive energies.

Activities and their relation to cation distribution in NiAl2O4 MgAl2O4 spinel solid solutions

The activity of NiAl2O4 in NiAl2O4MgAl2O4 solid solutions has been measured by using a solid oxide galvanic cell of the type, Pt, Ni + NiAl2O4 + Al2O3(α)/CaOZrO2/Ni + NixMg1−xAl2O4 + Al2O3(α). Pt, in the temperature range 750–1150°C. The activities in the spinel solid solutions show negative deviations from Raoult's law. The cation distribution in the solid solutions has been calculated using site preference energies independent of composition for Ni2+, Mg2+, and Al3+ ions obtained from crystal field theory and measured cation disorder in pure NiAl2O4 and MgAl2O4, and assumi g ideal mixing of cations on the tetrahedral and octahedral positions. The calculated values correctly predict the decrease in the fraction, α, of Ni2+ ions on tetrahedral sites for 1>x>0.25, observed by Porta et al. [J. Solid State Chem.11, 135 (1974)] but do not support their tentative evidence for an increase in α for x < 0.25. The measured excess free energy of mixing can be completely accounted for by using either the calculated or the measured cation distributions. This suggests that the Madelung energy is approximately a linear function of composition in the solid solutions. The composition of NiOMgO solid solutions in equilibrium with NiAl2O4MgAl2O4 solid solutions has been calculated from the results and information available in literature.

Solubility and activity of oxygen in liquid indium and copper indium alloys

The solubility of oxygen in liquid indium in the temperature range 650–820 °C and in liquid copper-indium alloys at 1100 °C in equilibrium with indium sesquioxide has been measured by a phase equilibration technique. The solubility of oxygen in pure indium is given by the relation log(at.% O) = −4726/T + 3.73 (±0.08) Using the recently measured values for the standard free energy of formation of In2O3 and assuming that oxygen obeys Sievert's law up to saturation, the standard free energy of solution of molecular oxygen in liquid indium is calculated as View the MathML sourceΔG°= −51 440 + 8.07 T (±500) cal where the standard state for dissolved oxygen is an infinitely dilute solution in which activity is equal to atomic per cent. The effect of indium additions on the activity coefficient of oxygen dissolved in liquid copper was measured by a solid oxide galvanic cell. The interaction parameter ϵ0In is given by View the MathML source The experimentally determined variation of the activity coefficient of oxygen in dilute solution in Cu-In alloys is in fair agreement with that predicted by a quasichemical model in which each oxygen atom is assumed to be interstitially coordinated to four metal atoms and the nearest neighbour metal atoms are assumed to lose approximately half their metallic cohesive energies.

Thermodynamics of oxide sulfate melts: The system PbO PbSO4

Activities in the PbO-PbSO4 melts at 1253 K have been measured by emf and gas-equilibration techniques. The activity of PbO was directly obtained from the emf of the solid oxide cell, Pt, Ni-NiO/CaO-ZrO2/Auo.92PbO.08, PbOx-PbSO4(1-x), Ir, Pt for 1.0 >XPbO > 0.6. The melt and the alloy were contained in closed zirconia crucibles. Since the partial pressure of SO2 gas in equilibrium with the melt and alloy was appreciable (>0.08 atm) atXPbO < 0.6, activities at lower PbO concentrations were derived from measurements of the weight gain of pure PbO under controlled gas streans of Ar + SO2 + O2. The partial and integral free energies of mixing at 1253 K were calculated and found to fit a subregular model: ΔGEPbO =X2PbSO4 {-42,450 + 20,000X2PbSO4} J mol-1 ΔGEPbO =X2pbSO {-12,450 - 20,000XPbS} J mol-1 ΔGEpbSOXPbSO4 {-32,450XPbS - 22,450XPbSO4 } J mol-1. The standard free energy of formation of liquid PbSO4 from pure liquid PbO and gaseous SO3 at 1 atm at 1253 K was evaluated as -88.02 (±0.72) kJ mol-1.