Thermodynamic characterization of ferric and ferrous haem binding to a designed four-alpha-helix protein

The thermodynamics of ferric and ferrous haem affinity of a de novo designed four-alpha-helix bundle protein and the associated haem electrochemistry is described.     

Exon deletions of the phenylalanine hydroxylase gene in Italian hyperphenylalaninemics

A consistent finding of many studies describing the spectrum of mutant phenylalanine hydroxylase (PAH) alleles underlying hyperphenylalaninemia is the impossibility of achieving a 100% mutation ascertainment rate using conventional gene-scanning methods. These methods include denaturing gradient gel electrophoresis (DGGE), denaturing high performance liquid chromatography (DHPLC), and direct sequencing. In recent years, it has been shown that a significant proportion of undetermined alleles consist of large deletions overlapping one or more exons. These deletions have been difficult to detect in compound heterozygotes using gene-scanning methods due to a masking effect of the non-deleted allele. To date, no systematic search has been carried out for such exon deletions in Italian patients with phenylketonuria or mild hyperphenylalaninemia. We used multiplex ligation- dependent probe amplification (MLPA), comparative multiplex dosage analysis (CMDA), and real-time PCR to search for both large deletions and duplications of the phenylalanine hydroxylase gene in Italian hyperphenylalaninemia patients. Four deletions removing different phenylalanine hydroxylase (PAH) gene exons were identified in 12 patients. Two of these deletions involving exons 4-5-6-7-8 (systematic name c.353-?_912 + ?del) and exon 6 (systematic name c.510-?_706 + ?del) have not been reported previously. In this study, we show that exon deletion of the PAH gene accounts for 1.7% of all mutant PAH alleles in Italian hyperphenylalaninemics.     

Interaction energies between tetrahydrobiopterin analogues and aromatic residues in tyrosine hydroxylase and phenylalanine hydroxylase

The phenylalanine residues 300 and 309 in the enzyme tyrosine hydroxylase are known to aid in the positioning and binding of tetrahydrobiopterin (BH4) to the enzyme active site. The residues phenylalanine 254 and tyrosine 325 similarly aid in binding BH4 in phenylalanine hydroxylase. BH4 is a cofactor necessary for enzyme function, and mutations in these residues have been shown to cause a decrease in enzyme function. We examine the pairwise interactions between each aromatic residue and BH4 using second-order Moller Plesset theory and density functional theory to determine the amount of binding due to these aromatic residues. Further, we perform in silico point mutations of these residues to determine if several likely mutations can cause a decrease in protein function. Our results show that dispersion dominates these interactions, and electrostatics alone is not enough to bind the BH4.     

Thermodynamic integration to predict host-guest binding affinities

An alchemical free energy method with explicit solvent molecular dynamics simulations was applied as part of the blind prediction contest SAMPL3 to calculate binding free energies for seven guests to an acyclic cucurbit-[n]uril host. The predictions included determination of protonation states for both host and guests, docking pose generation, and binding free energy calculations using thermodynamic integration. We found a root mean square error (RMSE) of 3.6 kcal mol(-1) from the reference experimental results, with an R(2) correlation of 0.51. The agreement with experiment for the largest contributor to this error, guest 6, is improved by 1.7 kcal mol(-1) when a periodicity-induced free energy correction is applied. The corrections for the other ligands were significantly smaller, and altogether the RMSE was reduced by 0.4 kcal mol(-1). We link properties of the host-guest systems during simulation to errors in the computed free energies. Overall, we show that charged host-guest systems studied here, initialized in unconfirmed docking poses, present a challenge to accurate alchemical simulation methods.     

Virtual screening for binding of phenylalanine analogues to phenylalanyl-tRNA synthetase

Although incorporation of nonnatural amino acids provides a powerful means of controlling protein structure and function, experimental investigations of amino acid analogues for utilization by the protein biosynthetic machinery can be costly and time-consuming. In this paper, we describe a computational protocol (HierDock) for predicting the relative energies of binding of phenylalanine analogues to phenylalanyl-tRNA synthetase (PheRS). Starting with the crystal structure of Thermus thermophilus PheRS without bound ligand, HierDock predicts the binding site of phenylalanine (Phe) within 1.1 A of that revealed by the crystal structure of PheRS cocrystallized with Phe. The calculated binding energies of Phe analogues in PheRS, using HierDock, correlate well with the translational activities of the same analogues in Escherichia coli. HierDock identifies p-fluorophenylalanine and 3-thienylalanine as especially good substrates for PheRS, in agreement with experiment. These results suggest that the HierDock protocol may be useful for virtual screening of amino acid analogues prior to experiment.     

Thermodynamic characterization of binding of DNA with cisplatin in aqueous solution by calorimetry

The behaviour of cis-diamminedichloroplatinum(II) (cisplatin) binding to DNA was studied thermodynamically by calorimetric methods such as flow microcalorimetry and differential scanning calorimetry (DSC). The thermodynamic quantities of binding of cisplatin to DNA were determined from the measurement of the heat of mixing. From the results obtained, it was suggested that the complex formation by the interaction of DNA with cisplatin may be influenced by the entropy term as a dominant factor. UV spectral measurement on solutions having a known concentration of DNA and cisplatin solutions of various concentrations was carried out at room temperature, and the difference of absorption, Δ A ₂₆₀ at wavelength 260 nm between DNA solutions with and without cisplatin was estimated. From the results obtained, a hyperchromic effect in the DNA solution containing cisplatin was found to exist. The appearance of the hyperchromic effect may be considered to originate from the disturbance of the base stacking between adjacent base pairs of DNA by the interaction of DNA with cisplatin. In addition, the thermal stability of the DNA-cisplatin complex was also studied by DSC method. The binding of cisplatin decreases the thermal stability of DNA; the transition temperature and the heat of the helix-coil transition of DNA decrease accompanying the binding of cisplatin. The decrease of the transition temperature is caused by the kinked DNA(helix') accompanying the appearance of the hyperchromic effect by binding cisplatin; also, the decrease of the heat of helix-coil transition may be based on the cooperative action between the heat of helix-coil transition of the kinked DNA(helix') and the heat of dissociation when cisplatin is dissociated from the DNA-cisplatin complex. By taking into consideration these results, the heat of binding of cisplatin to DNA was estimated to be about −106 kJ per mole of cisplatin.     

Thermodynamic characterization of the acetylacetone-trichloroethylene system

Delfini, M., Gironi, F. and Variali, G., 1984. Thermodynamic characterization of the acetylacetone-trichloroethylene system. Fluid Phase Equilibria, 18: 69–82.Vapor-liquid equilibria have been measured for the system acetylacetone-trichloroethylene at 100, 200, 400 and 760 mm Hg. The influence of trichloroethylene on the keto-enol equilibrium of acetylacetone has been elucidated by ¹H NMR spectroscopy.A semiempirical model taking into account the “true” chemical species involved (the enol and keto tautomers of acetylacetone, and trichloroethylene) is used for thermodynamic reduction of the experimental data.     

Thermodynamic characterization of NiAl

Thermodynamic properties of the high-stability intermetallic compound nickel aluminide, NiAl, have been determined from mass-spectrometric, weight-loss effusion, and calorimetric measurements, using samples from a single preparation with a composition determined to be Ni_0.986Al_1.014. Per mole of NiAl molecules, the specific heat capacity at room temperature of 298 K is 48.54 J · K^?1 · mol^?1, with a linear temperature dependence of +0.0104 J · K^?2 · mol^?1. At the same temperature, the enthalpy of formation is ?133.7 kJ · mol^?1, the entropy is about 53.8 J · K^?1 · mol^?1 and the enthalpy difference between room temperature and absolute zero is 7.97 kJ · mol^?1. The Gibbs free-energy is ?130.2 kJ · mol^?1 at T = 298 K, with a linear temperature dependence of +5.04 J · K^?1 · mol^?1. The Debye temperature is 452 K, while the electronic density-of-states at the Fermi-level is about 0.29 states per eV-atom. The NiAl⁺ ions were observed in the high-temperature mass spectra. Pressures for the gas at these temperatures were estimated and used with the results of quantum-mechanical calculations of total energy, specific heat, and entropy to calculate free-energy functions for the gas. These and additional results are compared with other measurements and discussed in terms of current theories of the electronic and structural properties of the compound.     

Thermodynamic characterization of chromium tellurate

The standard Gibbs energy of formation of chromium tellurate, Cr₂TeO₆ was determined from the vapour pressure measurement of TeO₂(g) over the phase mixture Cr₂TeO₆(s) + Cr₂O₃(s) in the temperature range 1,183–1,293 K. A thermogravimetry (TG)-based transpiration technique was used for the vapour pressure measurement. This technique was validated by measuring the vapour pressure of CdCl₂(g) over CdCl₂(s). The temperature dependence of the vapour pressure of CdCl₂(g) could be represented as logp (Pa) (±0.02) = 12.06 ? 8616.3/T (K) (734 ? 823 K). A ‘third-law’ analysis of the vapour pressure data yielded a mean value of 185.1 ± 0.4 kJ mol^?1 for the enthalpy of sublimation of CdCl₂(s). The temperature dependence of vapour pressure of TeO₂(g) generated by the incongruent vapourisation reaction, $ {\text{Cr}}_{ 2} {\text{TeO}}_{ 6} (\rm s) \to {\text{Cr}}_{ 2} {\text{O}}_{ 3} (\rm s) + {\text{TeO}}_{ 2} (\rm g) + 1/2\,{\text{O}}_{ 2} (\rm g) $ could be represented as logp (Pa) (±0.04) = 18.57 – 21,199/T (K) (1,183 – 1,293 K). The temperature dependence of the Gibbs energy of formation of Cr₂TeO₆ could be expressed as $ \{ \Updelta G_{\text{f}}^{ \circ } ({\text{Cr}}_{ 2} {\text{TeO}}_{ 6} ,{\text{ s}}){\text{ (kJ}}\,{\text{mol}}^{ - 1} )\pm 4. 0 {\text{\} = }} - 1 6 2 5. 6 { \,+\, 0} . 5 3 3 6\,T({\text{K}}) \, (1{,}183 - 1{,}293\,{\text{K}}). $ A drop calorimeter was used for measuring the enthalpy increments of Cr₂TeO₆ in the temperature range 373–973 K. Thermodynamic functions viz., heat capacity, entropy and Gibbs energy functions of Cr₂TeO₆ were derived from the experimentally measured enthalpy increment values. $ \Updelta H_{{{\text{f}},298\,{\text{K}}}}^{ \circ } ({\text{Cr}}_{ 2} {\text{TeO}}_{ 6} ) $ was found to be ?1636.9 ± 0.8 kJ mol^?1.     

Thermodynamic and kinetic aspects of metal binding to the histidine-rich protein, Hpn

The histidine-rich protein, Hpn, binds to essential metals Ni2+, Cu2+, Zn2+ and a therapeutic metal Bi3+ with the in vitro affinities in the order of Cu2+ > Ni2+ > Bi3+ > Zn2+. In contrast, the in vivo (in E. coli) protection by the protein is in the order of Ni2+ > Bi3+ > Cu2+ approximately Zn2+. The release of Ni2+ from the protein follows a two-step process consisting of a rapidly established equilibrium and subsequently a rate-determining step (dissociation of Hpn-Ni...EDTA to Ni-EDTA). Our work suggests the nickel storage and homeostasis in H. pylori as the primary role of Hpn.     

Thermodynamic characterization of carbon black-filled rubbers

Unfilled and carbon black-filled samples of synthetic isoprene- and butadiene-methylstyrenebased rubbers were characterized by precise heat capacity measurements in the temperature interval 4.2–300 K. Both unfilled samples proved to behave in an essentially fracton-like way in the temperature interval 6–30 K. The excess thermodynamic quantities derived from the smoothed data suggested that the thermodynamic state of the elastomeric phase in the filled rubbers was intrinsically unstable.     

Thermodynamic characterization of different actin isoforms

Summary The thermodynamic properties of the cardiac and skeletal a-actin isoforms were studied to characterize the molecular bases of the functional differences between them with the method of differential scanning calorimetry (DSC). The thermal properties of the actin filaments were described in the presence of calcium and magnesium ions as well. Based on the calculated free energy changes the α-cardiac actin filaments appeared to be more stable in its physiologically more relevant, magnesium saturated form. The magnesium saturated form of the α-cardiac actin filaments seemed to be more stable compared to the calcium saturated form of it. The enthalpy and entropy changes could differentiate between the α-cardiac and α-skeletal actin isoforms and between the calcium and magnesium saturated cardiac actin isoforms as well. Our results can demonstrate that the few differences between the amino acid sequences of the α-actin isoforms have an influence on the thermal properties and maybe on the function of these proteins as well.     

Thermodynamic parameters and counterion binding to the micelle in binary anionic surfactant systems

Competitive counterion binding of sodium and calcium to micelles, and mixed micellization have been investigated in the systems sodium dodecylsulfate (NaDS)/sodium decylsulfate (NaDeS) and NaDS/sodium 4-octylbenzenesulfonate (NaOBS) in order to accurately model the activity of the relevant species in solution. The critical micelle concentration (CMC) and equilibrium micelle compositions of mixtures of these anionic surfactants, which is necessary for determining fractional counterion binding measurements, is thermodynamically modeled by regular solution theory. The mixed micelle is ideal (the regular solution parameter β(M)=0) for the NaDS/NaOBS system, while the mixed micelle for NaDS/NaDeS has β(M)=-1.05 indicating a slight synergistic interaction. Counterion binding of sodium to the micelle is influenced by the calcium ion concentration, and vice versa. However, the total degree of counterion binding is essentially constant at approximately 0.65 charge negation at the micelle's surface. The counterion binding coefficients can be quantitatively modeled using a simple equilibrium model relating concentrations of bound and unbound counterions.     

Component B binding to the soluble methane monooxygenase hydroxylase by saturation-recovery EPR spectroscopy of spin-labeled MMOB

Spin-labeled Cys89 of the soluble methane monooxygenase regulatory protein (MMOB) from Methylococcus capsulatus (Bath) binds within 15 +/- 4 A of the hydroxylase (MMOH) diiron center, placing the MMOB docking site in the MMOH "canyon" region on iron-coordinating helices E and F of the alpha-subunit.     

Oxidation of methylated tetrahydropterins: Structure of the intial quinonoid-dihydropterin intermediate

The electerochemical oxidations of three methylated tetrahydropterins which, in 2 e⁻ −2 H⁺ reactons give quinonoid-dihydropterin intermediates having locked structures, have been studied. A comparison of the properties of these quinonoid-dihydropterin intermediates with those generated upon electrooxidation of the common tetrahydropterin pseudo-cofactors allows some conclusions to be drawn concerning the structure of the intermediate quinonoid-dihydropterins formed upon oxidation of the latter compounds.     

Thermodynamic characterization of asphaltene-resin interaction by microcalorimetry

This paper collects the work performed by isothermal titration calorimetry (ITC) to characterize the interaction between petroleum asphaltenes and resins. The interaction between these two fractions is of great interest in order to understand the mechanism of stabilization ofasphaltenes in crude oil. To simplify the approach, this preliminary study focuses on toluene solutions of both fractions. This paper reports the experimental determination of the average number of sites in asphaltene molecules and the enthalpy of interaction between asphaltenes and resins. Two models have been used to fit the experimental data. The enthalpies calculated by ITC are in the order of -2 to -4 kJ/mol. These values are in the limit of hydrogen bonding and permanent dipole energies. Similar values have been obtained by using the enthalpy as a fitting parameter in the SAFT equation.     

Thermodynamic characterization of the melting of a series of polyesteramides

The changes in enthalpy, entropy and volume upon melting have been determined by dilatometric and differential scanning calorimetry measurements for four polyesteramides of the type:

$\text{-[-}\text{COφCONH(CH}{}_2\text{)}{}_{\mathrm{n}}\text{}\text{NHCOφCOO(CH}{}_2\text{)}{}_{\mathrm{m}}\text{}\text{O}\text{-]-}{}_{\mathrm{x}}$

with the following values for n and m; 6-6, 12-2, 12-6 and 12-12. The changes in each state function vary quite regularly with the number of CH₂ groups/repeating unit. A comparison is made between experimental data on the entropy of fusion and theoretical predictions. There is emphasis on the influence on the thermodynamics of melting of the rigidity of the -OCO-φ-CONH- residues and, in particular, of the persistence in the molten state of many interchain hydrogen bonds.     

Thermodynamic analysis of the heterogenous binding sites of molecularly imprinted polymers

The thermodynamic interactions of two polymers, one Fmoc-L-Trp-imprinted (MIP), the other one an unimprinted reference (NIP), with the two Fmoc-tryptophan enantiomers were studied by frontal analysis, which allows accurate measurements of the adsorption isotherms. These isotherms were acquired at temperatures of 40, 50, 60, and 70 degrees C, for sample concentrations ranging between 0.005 and 40 mM. The mobile phase used was acetonitrile with one percent acetic acid as an organic modifier. Within the measured concentration ranges, the tri-Langmuir isotherm model accounts best for the isotherm data of both enantiomers on the MIP, the bi-Langmuir model for the isotherm data of Fmoc-L-Trp on the NIP. These isotherm models were selected using three independent processes: statistical tests on the results from regression of the isotherm data to different isotherm models; calculation of the affinity energy distribution from the raw isotherm data; comparison of the experimental and the calculated band profiles. The isotherm parameters obtained from these best selected isotherm models showed that the enantiomeric selectivity does not change significantly with temperature, while the affinity of the substrates for both the MIP and the NIP decrease considerably with increasing temperatures. These temperature effects on the binding performance of the MIP were clarified by considering the thermodynamic functions (i.e., the standard molar Gibbs free energy, the standard molar entropy of adsorption, and the standard molar enthalpy of adsorption) for each identified type of adsorption sites, derived from the Van't Hoff equation. This showed that the entropy of transfer of Fmoc-L-Trp from the mobile to the MIP stationary phase is the dominant driving force for the selective adsorption of Fmoc-L-Trp onto the enantioselective binding sites. This entropy does not change significantly with increasing temperatures from 40 to 70 degrees C.