Dipole moment of alamethicin as related to voltage-dependent conductance in lipid bilayers.

The dipole moment of alamethicin, which produces voltage-dependent conductance in lipid-bilayer membranes, was measured in mixed solvents of ethanol and dioxane. The value of the dipole moment was found to increase from 40 to 75 DU (Debye units), as the concentration of ethanol increased from 0 (pure dioxane) to 40%. The relaxation frequency of alamethicin also changes from 10 to 40 MHz, depending upon the concentration of ethanol in mixed solvents. The length of alamethicin was calculated by using the relaxation time and was found to range from approximately 40 to 20 A. The dipole moment was independently calculated from voltage-dependent conductance and compared with the measured value. The calculated value was found to be larger than the value of direct measurements, indicating that several alamethicin molecules are required to form a conducting pore and that their dipole moments are oriented parallel to each other.     

Use of protein database for the computation of the dipole moments of normal and abnormal hemoglobins.

Previously, we discussed the calculation of the dipole moments of small proteins using the three-dimensional protein data-base. Our results demonstrate that the calculated dipole moments are in acceptable agreement with measured values. We, however, noted the difficulty of the calculation with larger proteins, in particular those consisting of several subunits. Hemoglobin (Hb) is a protein having a molecular weight of 64,000 that consists of four subunits, a typical case where the computation was found to be difficult. To circumvent the difficulties, we calculated the dipole moment of each subunit separately. The dipole moment of the whole protein was calculated by the vectorial summation of subunit moments. With this method, the calculated net dipole moment is in good agreement with the experimental value. Our calculation shows that the dipole moment vectors of subunits are, by and large, antiparallel in tetramers causing partial cancellation of the net dipole moment. In addition to normal HbA, the dipole moment of abnormal HbS was calculated using an approximate computational technique. Because of the loss of two negative changes as a result of the replacement of glutamic acid with valine in beta-chains, the dipole moment of HbS was found, experimentally and theoretically, to be significantly smaller than that of HbA.     

On the thermodynamic characterization of membrane gating particles by their Boltzmann distribution

The characterizations of gating particles of ionic channels in nerve membranes by their equivalent valencies and their electric dipole moment changes are compared. The gating particle is represented as a system of electric charges in fixed positions in an external electric field and the potential energy of such a system is calculated in the approximation of a constant electric field. The proper expression of the Boltzmann distribution of the gating particles is presented. It is shown that the dipole moment of transition of the gating particle is the only proper thermodynamic (macroscopic) characteristics of the gating particles based on the available experimental information and does not depend on any microscopic assumption as the equivalent valency does.     

Heat denaturation of immunoglobin G in monomolecular layers

Studies were carried out of viscous-elastic properties of monomolecular layers of human immunoglobulin IgG formed at the interface water solutions of NaCl--air within 20 degrees C to 50 degrees C at NaCl concentration in sublayer from 0.3 to 1.0 M. It has been shown that at concentrations from 0.3 to 0.5 M of NaCl IgG macromolecules keep the tertiary structure, and in the region 35 +/- 5 degrees C a conformation transition is observed. The recorded conformation transition is reversible and of entropy nature. At NaCl concentration 0.75 in the sublayer and temperature close to 35 degrees C IgG macromolecules undergo irreversible structural changes due to the destruction of hydrogen and disulfide bonds in IgG molecules. Macromolecules dissociate to fragments with molecular mass 49,000 +/- 2000. At NaCl concentration 1.0 M and temperatures 30-50 degrees C IgG macromolecules of the monolayer are in a dissociated state. Changes in entropy, enthalpy and heat capacity as well as areas occupied by the macromolecules at dense packing, molecular mass and efficient electric dipole moment of the monolayer are calculated.     

Barrier to rotation and conformation of the -NR2 group in cytosine and its derivatives. Part II. Experimental and theoretical dipole moments of methylated cytosines.

The dipole moments of several cytosine, methylaminocytosine and dime-thylaminocytosine derivatives with and without an ortho methyl group were determined experimentally in dioxane and benzene. Calculations of total energies and dipole moments were performed by the CNDO/2 and INDO methods for sp2 and sp3 hybridization of exocyclic nitrogen for different values of rotational angle phiC-N. Comparison of the experimental dipole moments with those calculated for the energy minima suggests that the conformation of the dimethylamino group is not planar and differs from that found in cytosine. 1,5,7-Trimethylcytosine, with the dipole moment of 7 Deby units, was considered to be the model compound which closely reproduces the dipole moment of cytosine.     

Potentiometric titration of poly-L-lysine: the coil-to-beta transition

We have performed potentiometric titrations of poly-L -lysine. From these data we have calculated the free energy and enthalpy changes for the folding of the random coil to the α-helix in 10% ethanol (?120 and ?120 cal/mole) and from the random coil to the β-structure in water (?140 and 870 cal/mole) and in 10% ethanol (?180 and 980 cal mole). Comparison of these values with each other and with values for the coil → α- helix transition in water (?78 and ?880 cal/mole) led to the following conclusions. The stabilization by ethanol of ethanol of the α-helix with respect to the coil is that predicted from the known free energy of transfer of the peptide group from water to 10% ethanol. Similar data to explain the enthalpy difference are not available. The thermodynamic functions for the transition from α-helix to β-structure, obtained by subtracting those for the coil → α-helix and coil → β-structure transitions, are explained from a consideration of the structural differences: non bonded interactions of the polypeptide backbone are less favorable in the β-structure than in the α-helix, causing an increase in the energy, while hydrophobic contacts between side chains raise the entropy of the β-structure as compared with the α-helix, so that the free energy difference between the two structures is small, but enthalpy and entropy differences are large. The observation of only small differences in the free energy and enthalpy changes for the transition from coil β-structure upon going from water to 10% ethanol is expected by considering both the free energy of transfer of the peptide group (as for the α-helix) and the free energy and enthalpy of transfer of the apolar part of the side chain involved in hydrophobic bond formation.     

Calculation and measurement of the dipole moment of small proteins: Use of protein data base

The dipole moments of small protein molecules were determined experimentally in order to validate the calculated dipole moments by previous investigators. We found that the agreements are satisfactory for some proteins. There are, however, many proteins for which the agreement is less than satisfactory. In order to find the cause of the disagreement, the dipole moments of these proteins were recalculated using the Brookhaven Protein Data Bank. We calculated the dipole moment due to fixed surface charges and the bond moments of all the carbonyl groups in main chain and side chains. The calculation consists of the mean moments and their mean square fluctuations. In addition, we investigated the effect of electrostatic interactions between charged sites for several proteins. These results show that incorporation of the interactions does not affect substantially the calculated dipole moments. The rms fluctuation of the dipole moment is found to be small but not negligible. In conclusion, recalculated dipole moments are in good agreement with the observed values. © 1993 John Wiley & Sons, Inc.     

The electric dipole moment of DNA-binding HU protein calculated by the use of NMR database

Electric birefringence measurements indicated the presence of a large permanent dipole moment in HU protein–DNA complex. In order to substantiate this observation, numerical computation of the dipole moment of HU protein homodimer was carried out by using NMR protein databases. The dipole moments of globular proteins have hitherto been calculated with X-ray databases and NMR data have never been used before. The advantages of NMR databases are: (a) NMR data are obtained, unlike X-ray databases, using protein solutions. Accordingly, this method eliminates the bothersome question as to the possible alteration of the protein structure due to the transition from the crystalline state to the solution state. This question is particularly important for proteins such as HU protein which has considerable internal flexibility’s; (b) the three dimensional coordinates of hydrogen atoms in protein molecules can be determined with a sufficient resolution and this enables the N–H as well as C=O bond moments to be calculated. Since the NMR database of HU protein from Bacillus stearothermophilus consists of 25 models, the surface charge as well as the core dipole moments were computed for each of these structures. The results of these calculations show that the net permanent dipole moments of HU protein homodimer is approximately 500–530 D (1 D=3.33×10⁻³⁰ Cm) at pH 7.5 and 600–630 D at the isoelectric point (pH 10.5). These permanent dipole moments are unusually large for a small protein of the size of 19.5 kDa. Nevertheless, the result of numerical calculations is compatible with the electro-optical observation, confirming a very large dipole moment in this protein.     

Thermodynamic analysis of fast stages of specific lesion recognition by DNA repair enzymes

The methodology of determination of the thermodynamic parameters of fast stages of recognition and cleavage of DNA substrates is described for the enzymatic processes catalyzed by DNA glycosylases Fpg and hOGG1 and AP endonuclease APE1 during base excision repair (BER) pathway. For this purpose, stopped-flow pre-steady-state kinetic analysis of tryptophan fluorescence intensity changes in proteins and fluorophores in DNA substrates was performed at various temperatures. This approach made it possible to determine the changes of standard Gibbs free energy, enthalpy, and entropy of sequential steps of DNA-substrate binding, as well as activation enthalpy and entropy for the transition complex formation of the catalytic stage. The unified features of mechanism for search and recognition of damaged DNA sites by various enzymes of the BER pathway were discovered.     

Cold adaptation of enzyme reaction rates

A major issue for organisms living at extreme temperatures is to preserve both stability and activity of their enzymes. Cold-adapted enzymes generally have a reduced thermal stability, to counteract freezing, and show a lower enthalpy and a more negative entropy of activation compared to mesophilic and thermophilic homologues. Such a balance of thermodynamic activation parameters can make the reaction rate decrease more linearly, rather than exponentially, as the temperature is lowered, but the structural basis for rate optimization toward low working temperatures remains unclear. In order to computationally address this problem, it is clear that reaction simulations rather than standard molecular dynamics calculations are needed. We have thus carried out extensive computer simulations of the keto-enol(ate) isomerization steps in differently adapted citrate synthases to explore the structure-function relationships behind catalytic rate adaptation to different temperatures. The calculations reproduce the absolute rates of the psychrophilic and mesophilic enzymes at 300 K, as well as the lower enthalpy and more negative entropy of activation of the cold-adapted enzyme, where the latter simulation result is obtained from high-precision Arrhenius plots. The overall catalytic effect originates from electrostatic stabilization of the transition state and enolate and the reduction of reorganization free energy. The simulations, however, show psychrophilic, mesophilic, and hyperthermophilic citrate synthases to have increasingly stronger electrostatic stabilization of the transition state, while the energetic penalty in terms of internal protein interactions follows the reverse order with the cold-adapted enzyme having the most favorable energy term. The lower activation enthalpy and more negative activation entropy observed for cold-adapted enzymes are found to be associated with a decreased protein stiffness. The origin of this effect is, however, not localized to the active site but to other regions of the protein structure.     

Double-stranded structure for hyaluronic acid in ethanol-aqueous solution as revealed by circular dichroism of oligomers

The sigmoidal nature of circular dichroism (CD) changes for hyaluronic acid solutions as a function of solvent composition or temperature is studied as a function of chain length by using oligomers. We find a chain length effect with approximately nine disaccharides required for the structural transition as a function of organic solvent, which proves that the transition is cooperative with large transition enthalpy and entropy. The transition also depends on sample concentration as expected for strand association, and this was investigated in detail for oligomers 12 and 16 disaccharides long. Indeed, it was possible to prevent completely the transition in mixed solvent with sufficient dilution of these oligomers, which demonstrates strand association. The CD data in mixed solvent as a function of oligomer concentration were fit with various models for association of two and more strands. Simplex methods were used to investigate the vector space of unknowns for the models, and two-strand models were shown to consistently give a better fit. A cooperative two-strand zipper model which allows relative sliding of the chains had the smallest fitting error and produced the following thermodynamic parameters (in terms of a duplex of disaccharide units) for the ordered structure in an aqueous solution containing 45% v/v ethanol, 12.5 mM NaH2PO4, and 7.5 mM H3PO4: enthalpy of growth, -1.0 +/- 0.3 kcal mol-1; entropy of growth, -2.3 +/- 1.3 eu mol-1; enthalpy of initiation, -20 +/- 3 kcal mol-1; entropy of initiation, -71 +/- 15 eu mol-1. The results are consistent with a double-stranded and helical structure for hyaluronic acid in solutions of reduced dielectric constant.     

Interaction of phloretin with membranes: on the mode of action of phloretin at the water-lipid interface

 The interaction of phloretin with single lipid bilayers on a spherical support and with multilamellar vesicles was studied by differential scanning calorimetry (DSC) and nuclear magnetic resonance (NMR). The results indicated that phloretin interacts with the lipid layer and changes its structural parameters. In DSC experiments, phloretin in its neutral form strongly decreased the lipid phase transition temperature and slightly reduced the cooperativity of the phase transition within the lipid layer. In NMR measurements, phloretin led to an increase of the transverse relaxation time constant but had no effect on the spin-lattice relaxation time constant. The overall dipole moment of phloretin was experimentally determined and was found to be roughly 40% lower than has been published previously. This result suggested that the size of the dipole moment of phloretin does not provide such a high contribution to the effect of phloretin on the dipole potential of monolayers and bilayers as has been published previously. To understand the discrepancy between phloretin adsorption and dipole potential change, we performed computational conformational analysis of phloretin in the gas phase. The results showed that a wide distribution of the dipole moments of phloretin conformers exists, which mainly depends on the orientation of the OH moieties. The adsorption of phloretin as determined from its binding to solid supported bilayers differed from the one determined from dipole potential measurements on black lipid membranes. The difference between the phloretin dissociation constants of both types of experiments suggested a change of its dipole moment normal to the membrane surface in a concentration-dependent manner, which was in agreement with the results of the computational conformational analysis. Received: 21 June 1999 / Revised version: 7 January 2000 / Accepted: 31 March 2000     

Thermodynamic Parameters of Frog Brain κ-Opioid Receptors

Abstract: The thermodynamic parameters for [³H]-ethylketocyclazocine binding in frog ( Rana esculenta ) brain membranes have been examined. Computer-based nonlinear regression analysis of the untransformed equilibrium displacement data showed that this ligand bound to two sites with different affinities and capacities in this tissue. K _A values derived from equilibrium displacement curves have been used for calculating the changes in the standard Gibbs energy, enthalpy, and entropy during the binding process. Van't Hoff plots are bipartite, with transitions occurring at 18°C for both the high- and the low-affinity sites. For the high-affinity site, the reaction appears to be associated with a decrease in enthalpy below the transition temperature and a significant gain in entropy above this temperature. The reverse appears to be true for the low-affinity site. We conclude that this profile fairly approximates the mixed agonist-antagonist nature of this ligand and surmise that thermodynamic analysis could be a very useful tool for characterization of the nature of cloned opioid receptors in vitro.     

Effects of hydrated water on protein unfolding

The conformational stability of a protein in aqueous solution is described in terms of the thermodynamic properties such as unfolding Gibbs free energy, which is the difference in the free energy (Gibbs function) between the native and random conformations in solution. The properties are composed of two contributions, one from enthalpy due to intramolecular interactions among constituent atoms and chain entropy of the backbone and side chains, and the other from the hydrated water around a protein molecule. The hydration free energy and enthalpy at a given temperature for a protein of known three-dimensional structure can be calculated from the accessible surface areas of constituent atoms according to a method developed recently. Since the hydration free energy and enthalpy for random conformations are computed from those for an extended conformation, the thermodynamic properties of unfolding are evaluated quantitatively. The evaluated hydration properties for proteins of known transition temperature (Tm) and unfolding enthalpy (delta Hm) show an approximately linear dependence on the number of constituent heavy atoms. Since the unfolding free energy is zero at Tm, the enthalpy originating from interatomic interactions of a polypeptide chain and the chain entropy are evaluated from an experimental value of delta Hm and computed properties due to the hydrated water around the molecule at Tm. The chain enthalpy and entropy thus estimated are largely compensated by the hydration enthalpy and entropy, respectively, making the unfolding free energy and enthalpy relatively small. The computed temperature dependences of the unfolding free energy and enthalpy for RNase A, T4 lysozyme, and myoglobin showed a good agreement with the experimental ones.(ABSTRACT TRUNCATED AT 250 WORDS)     

Kauzmann's paradox and the glass transition

Kauzmann showed that the entropy of a liquid decreases rapidly on cooling towards the kinetic glass transition temperature and extrapolates to unreasonable values at lower temperature. The temperature where the extrapolated liquid entropy meets the crystal entropy is now called the Kauzmann temperature. Thermodynamics, with Planck's statement of the third law, shows that the entropy of a liquid cannot be less than the entropy of a glass with the same enthalpy. This is the thermodynamic condition violated by the Kauzmann extrapolation and it suggests a thermodynamic glass transition. Simulations show that, for the simple models studied and regardless of how the liquid entropy is extrapolated, the Kauzmann temperature cannot be reached because the entropy of glasses with the same enthalpy as the liquid is greater than that of the crystal.     

Investigations on spectra and orientation of dipole moments of uracil and thymine by electrochromism

The direction of the ground stale dipole moment with respect to the transition moment to the lowest excited singlet state as well as the dipole moment in this excited state could be determined from the influence of an electric field on the light absorption of uracil and thymine in solution. By making use of results on the orientation of the transition moment in the molecular framework, the orientation of the ground-and excited-state dipole moments can also be fixed and compared with theoretical predictions. The agreement is fair. The measurements show that in both compounds a weak band is hidden under the longest-wavelength absorption band.     

Thermodynamic activation properties of elongation factor 2 (EF-2) proteins from psychrotolerant and thermophilic Archaea

In this study, the thermodynamic activation parameters of cold-adapted proteins from Archaeaa are described for the first time for the irreversible protein unfolding and ribosome-dependent GTPase activity of elongation factor 2 (EF-2) from the psychrotolerant Methanococcoides burtonii and the thermophilic Methanosarcina thermophila. Thermolability of Methanococcoides burtonii EF-2 was demonstrated by a low activation free-energy of unfolding as a result of low activation-enthalpy. Although structural data for EF-2 are presently limited to protein homology modeling, the observed thermodynamic properties are consistent with a low number of noncovvalent bonds or an altered solvent interaction, causing a loss of entropy during the unfolding process. A physiological concentration of potassium aspartate or potassium glutamate was shown to stabilize both proteins against irreversible denaturation by strengthening noncovalent interactions, as indicated by increased activation enthalpies. The transition state of GTPase activity for Methanococcoides burtonii EF-2 was characterized by a lower activation enthalpy than for Methanosarcina thermophila EF-2. The relative entropy changes could be explained by differential displacement of water molecules during catalysis, resulting in similar activation free energies for both proteins. The presence of solutes was shown to facilitate the breaking of enthalpy-driven interactions and structuring of more water molecules during the reaction. By studying the thermodynamic activation parameters of both GTPase activity and unfolding and examining the effects of intracellular solutes and partner proteins (ribosomes), we were able to identify enthalpic and entropic properties that have evolved in the archaeal EF-2 proteins to enable Methanococcoides burtonii and Methanosarcina thermophila to adapt to their respective thermal environments.     

Muscarinic acetylcholine receptor: thermodynamic analysis of the interaction of agonists and antagonists

The thermodynamic parameters of the interaction of agonists and antagonists with heart and brain muscarinic receptors were determined. The binding of quinuclidinyl [3H]benzilate and the inhibition of quinuclidinyl benzilate (QNB) binding by agonists and antagonists were examined at temperatures between 2 degrees C and 27 degrees C. The density of specific binding sites and the relative proportions of high- and low-affinity binding components of drugs were unaffected by the temperature changes. The binding of atropine was entropy driven in brain and heart membranes. In contrast, net values of these thermodynamic parameters for QNB binding and for the high-affinity binding component of pirenzepine to brain membranes were decreased with the enhancement of the temperature. The low-affinity binding component of the agonists carbachol, oxotremorine and pilocarpine was enthalpy driven. Their high-affinity binding component was entropy driven at 2 degrees C and became enthalpy driven when the incubation temperature was increased. The guanine nucleotide Gpp[NH]p partly prevented the temperature-dependent decrease of net entropy and enthalpy values. Considering that the net changes of thermodynamic parameters are relevant of the interactions between the ligand, the receptor protein and the adjoining membranous molecules, a three-state conformational model is proposed for the muscarinic receptor protein. The receptor selectivity is reappreciated owing to these three states of the receptor protein and the different components of the muscarinic receptor complexes.