A molecular dynamics study based post facto free energy analysis of the binding of bovine angiogenin with UMP and CMP ligands

Angiogenin is a protein belonging to the superfamily of RNase A. The RNase activity of this protein is essential for its angiogenic activity. Although members of the RNase A family carry out RNase activity, they differ markedly in their strength and specificity. In this paper, we address the problem of higher specificity of angiogenin towards cytosine against uracil in the first base binding position. We have carried out extensive nano-second level molecular dynamics(MD) computer simulations on the native bovine angiogenin and on the CMP and UMP complexes of this protein in aqueous medium with explicit molecular solvent. The structures thus generated were subjected to a rigorous free energy component analysis to arrive at a plausible molecular thermodynamic explanation for the substrate specificity of angiogenin.

Estimation of surface free energy of pyrites by contact angle measurements

The surface properties of coal-pyrite play a major role in determining its separation from coal in processes such as flotation. The solution pH is an important parameter in determining the surface properties of both coal and coal-pyrite such as surface free energy and zeta-potential. In the present investigation, the effect of pH on the surface free energy of pyrites from different sources was studied. The surface free energy of solids is made up of two components, i.e. the dispersive surface free energy and the acid-base interaction energy. Various methods have been used by previous researchers to evaluate these two components for different solids. In the present study, a new approach was developed and used to study the surface free energy of pyrite surfaces. Results indicate that the dispersion surface free energy of various pyrites is independent of pH while the acid-base interaction energy is strongly dependent on the pH. The acid-base interaction energy is different for each pyrite sample and also the change with pH varies with the type of pyrite. Coal-pyrite was found to be more hydrophobic than ore-pyrite which may be attributed to the presence of carbon in coal-pyrites. The acid-base interaction energy varied little with pH for coal pyrites than ore-pyrite. Comparison of acid-base interaction energy with zeta-potential measurements shows a good correlation between the minimum in acid-base interaction energy and the pHpzc.

Understanding glassy dynamics from the free-energy landscape

Many interesting features of the dynamics of simple liquids near the glass transition may be understood in terms of properties of the free-energy landscape obtained from numerical studies of a model free-energy functional. Main results obtained from this approach are summarized and a list of references to relevant publications is provided. (C) 2002 Elsevier Science B.V. All rights reserved.

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.

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.

Free Energy Barriers for Escape of Water Molecules from Protein Hydration Layer

Free energy barriers separating interfacial water molecules from the hydration layer at the surface of a protein to the bulk are obtained by using the umbrella sampling method of free energy calculation. We consider hydration layer of chicken villin head piece (HP-36) which has been studied extensively by molecular dynamics simulations. The free energy calculations reveal a strong sensitivity to the secondary structure. In particular, we find a region near the junction of first and second helix that contains a cluster of water molecules which are slow in motion, characterized by long residence times (of the order of 100 ps or more) and separated by a large free energy barrier from the bulk water. However, these ``slow'' water molecules constitute only about 5-10% of the total number of hydration layer water molecules. Nevertheless, they play an important role in stabilizing the protein conformation. Water molecules near the third helix (which is the important helix for biological function) are enthalpically least stable and exhibit the fastest dynamics. Interestingly, barrier height distributions of interfacial water are quite broad for water surrounding all the three helices (and the three coils), with the smallest barriers found for those near the helix-3. For the quasi-bound water molecules near the first and second helices, we use well-known Kramers' theory to estimate the residence time from the free energy surface, by estimating the friction along the reaction coordinate from the diffusion coefficient by using Einstein relation. The agreement found is satisfactory. We discuss the possible biological function of these slow, quasi-bound (but transient) water molecules on the surface.

Characterization of structural and free energy properties of promoters associated with Primary and Operon TSS in Helicobacter pylori genome and their orthologs

Promoter regions in the genomes of all domains of life show similar trends in several structural properties such as stability, bendability, curvature, etc. In current study we analysed the stability and bendability of various classes of promoter regions (based on the recent identification of different classes of transcription start sites) of Helicobacter pylori 26695 strain. It is found that primary TSS and operon-associated TSS promoters show significantly strong features in their promoter regions. DNA free-energy-based promoter prediction tool PromPredict was used to annotate promoters of different classes, and very high recall values (similar to 80%) are obtained for primary TSS. Orthologous genes from other strains of H. pylori show conservation of structural properties in promoter regions as well as coding regions. PromPredict annotates promoters of orthologous genes with very high recall and precision.

Free energy barriers for homogeneous crystal nucleation in a eutectic system of binary hard spheres

In this study, the free energy barriers for homogeneous crystal nucleation in a system that exhibits a eutectic point are computed using Monte Carlo simulations. The system studied is a binary hard sphere mixture with a diameter ratio of 0.85 between the smaller and larger hard spheres. The simulations of crystal nucleation are performed for the entire range of fluid compositions. The free energy barrier is found to be the highest near the eutectic point and is nearly five times that for the pure fluid, which slows down the nucleation rate by a factor of 10(-31). These free energy barriers are some of highest ever computed using simulations. For most of the conditions studied, the composition of the critical nucleus corresponds to either one of the two thermodynamically stable solid phases. However, near the eutectic point, the nucleation barrier is lowest for the formation of the metastable random hexagonal closed packed (rhcp) solid phase with composition lying in the two-phase region of the phase diagram. The fluid to solid phase transition is hypothesized to proceed via formation of a metastable rhcp phase followed by a phase separation into respective stable fcc solid phases.

Gibbs free energy of formation of rhodium sulfides

Using a solid-state electrochemical technique, thermodynamic properties of three sulfide phases (RhS0.882, Rh3S4, Rh2S3) in the binary system (Rh + S) are measured as a function of temperature over the range from (925 to 1275) K. Single crystal CaF2 is used as the electrolyte. The auxiliary electrode consisting of (CaS + CaF2) is designed in such a way that the sulfur chemical potential converts into an equivalent fluorine potential at each electrode. The sulfur potentials at the measuring electrodes are established by the mixtures of (Rh + RhS0.882), (RhS0.882 + Rh3S4) and (Rh3S4 + Rh2S3) respectively. A gas mixture (H-2 + H2S + Ar) of known composition fixes the sulfur potential at the reference electrode. A novel cell design with physical separation of rhodium sulfides in the measuring electrode from CaS in the auxiliary electrode is used to prevent interaction between the two sulfide phases. They equilibrate only via the gas phase in a hermetically sealed reference enclosure. Standard Gibbs energy changes for the following reactions are calculated from the electromotive force of three cells: 2.2667Rh (s) + S-2 (g) -> 2.2667RhS(0.882) (s), Delta(r)G degrees +/- 2330/(J . mol(-1)) = -288690 + 146.18 (T/K), 4.44RhS(0.882) (s) + S-2 (g) -> 1.48Rh(3)S(4) (s), Delta(r)G degrees +/- 2245/(J . mol(-1)) = -245596 + 164.31 (T/K), 4Rh(3)S(4) (s) + S-2 (g) -> 6Rh(2)S(3) (s), Delta(r)G degrees +/- 2490/(J . mol(-1)) = -230957 + 160: 03 (T/K). Standard entropy and enthalpy of formation of rhodium sulfides from elements in their normal standard states at T = 298.15 K are evaluated. (C) 2013 Elsevier Ltd. All rights reserved.

Propensity to Form Amyloid Fibrils Is Encoded as Excitations in the Free Energy Landscape of Monomeric Proteins

Protein aggregation, linked to many of diseases, is initiated when monomers access rogue conformations that are poised to form amyloid fibrils. We show, using simulations of src SH3 domain, that mechanical force enhances the population of the aggregation-prone (N*) states, which are rarely populated under force free native conditions but are encoded in the spectrum of native fluctuations. The folding phase diagrams of SH3 as a function of denaturant concentration (C]), mechanical force (f), and temperature exhibit an apparent two-state behavior, without revealing the presence of the elusive N* states. Interestingly, the phase boundaries separating the folded and unfolded states at all C] and f fall on a master curve, which can be quantitatively described using an analogy to superconductors in a magnetic field. The free energy profiles as a function of the molecular extension (R), which are accessible in pulling experiments, (R), reveal the presence of a native-like N* with a disordered solvent-exposed amino-terminal beta-strand. The structure of the N* state is identical with that found in Fyn SH3 by NMR dispersion experiments. We show that the timescale for fibril formation can be estimated from the population of the N* state, determined by the free energy gap separating the native structure and the N* state, a finding that can be used to assess fibril forming tendencies of proteins. The structures of the N* state are used to show that oligomer formation and likely route to fibrils occur by a domain-swap mechanism in SH3 domain. (C) 2014 Elsevier Ltd. All rights reserved.

Multidimensional free energy surface of unfolding of HP-36: Microscopic origin of ruggedness

The protein folding funnel paradigm suggests that folding and unfolding proceed as directed diffusion in a multidimensional free energy surface where a multitude of pathways can be traversed during the protein's sojourn from initial to final state. However, finding even a single pathway, with the detail chronicling of intermediates, is an arduous task. In this work we explore the free energy surface of unfolding pathway through umbrella sampling, for a small globular a-helical protein chicken-villin headpiece (HP-36) when the melting of secondary structures is induced by adding DMSO in aqueous solution. We find that the unfolding proceeds through the initial separation or melting of aggregated hydrophobic core that comprises of three phenylalanine residues (Phe7, Phe11, and Phe18). This separation is accompanied by simultaneous melting of the second helix. Unfolding is found to be a multistage process involving crossing of three consecutive minima and two barriers at the initial stage. At a molecular level, Phe18 is observed to reorient itself towards other hydrophobic grooves to stabilize the intermediate states. We identify the configuration of the intermediates and correlate the intermediates with those obtained in our previous works. We also give an estimate of the barriers for different transition states and observe the softening of the barriers with increasing DMSO concentration. We show that higher concentration of DMSO tunes the unfolding pathway by destabilizing the third minimum and stabilizing the second one, indicating the development of a solvent modified, less rugged pathway. The prime outcome of this work is the demonstration that mixed solvents can profoundly transform the nature of the energy landscape and induce unfolding via a modified route. A successful application of Kramer's rate equation correlating the free energy simulation results shows faster rate of unfolding with increasing DMSO concentration. This work perhaps presents the first systematic theoretical study of the effect of a chemical denaturant on the microscopic free energy surface and rates of unfolding of HP-36. (C) 2014 AIP Publishing LLC.

Gibbs Energy of Formation of Cobalt Divanadium Tetroxide

The Gibbs energy of formation of V2O3-saturated spinel CoV2O4 has been measured in the temperature range 900–1700 K using a solid state galvanic cell, which can be represented as Pt, Co + CoV2O4 + V2O3/(CaO) ZrO2/Co + CoO, Pt. The standard free energy of formation of cobalt vanadite from component oxides can be represented as CoO (rs) + V2O3 (cor) → CoV2O4 (sp), ΔG° = −30,125 − 5.06T (± 150) J mole−1. Cation mixing on crystallographically nonequivalent sites of the spinel is responsible for the decrease in free energy with increasing temperature. A correlation between “second law” entropies of formation of cubic 2–3 spinels from component oxides with rock salt and corundum structures and cation distribution is presented. Based on the information obtained in this study and trends in the stability of aluminate and chromite spinels, it can be deduced that copper vanadite is unstable.