Deciphering the role of the electrostatic interactions in the alpha-tropomyosin head-to-tail complex

Skeletal alpha-tropomyosin (Tm) is a dimeric coiled-coil protein that forms linear assemblies under low ionic strength conditions in vitro through head-to-tail interactions. A previously published NMR structure of the Tin head-to-tail complex revealed that it is formed by the insertion of the N-terminal coiled-coil of one molecule into a cleft formed by the separation of the helices at the C-terminus of a second molecule. To evaluate the contribution of charged residues to complex stability, we employed single and double-mutant Tm fragments in which specific charged residues were changed to alanine in head-to-tail binding assays, and the effects of the mutations were analyzed by thermodynamic double-mutant cycles and protein-protein docking. The results show that residues K5, K7, and D280 are essential to the stability of the complex. Though D2, K6, D275, and H276 are exposed to the solvent and do not participate in intermolecular contacts in the NMR structure, they may contribute to head-to-tail complex stability by modulating the stability of the helices at the Tm termini.

Solvent assisted decomposition of the tetrahedral intermediate of the transesterification reaction to biodiesel production. A density functional study

B3LYP/6-31 + G(d) calculations were employed to investigate the mechanism of the transesterification reaction between a model monoglyceride and the methoxide and ethoxide anions. The gas-phase results reveal that both reactions have essentially the same activation energy (5.9 kcal mol(-1)) for decomposition of the key tetrahedral intermediate. Solvent effects were included by means of both microsolvation and the polarizable continuum solvation model CPCM. Both solvent approaches reduce the activation energy, however, only the microsolvation model is able to introduce some differentiation between methanol and ethanol, yielding a lower activation energy for decomposition of the tetrahedral intermediate in the reaction with methanol (1.1 kcal mol(-1)) than for the corresponding reaction with ethanol (2.8 kcal mol(-1)), in line with experimental evidences. Analysis of the individual energy components within the CPCM approach reveals that electrostatic interactions are the main contribution to stabilization of the transition state. (C) 2009 Elsevier Ltd. All rights reserved.

Properties and one-step synthesis of (2-acetylpyridine)tetraammineruthenium(II), [Ru-II(2-acpy)(NH3)(4)](2+) and tetraammine(2-benzoylpyridine)ruthenium(II), [Ru-II(NH3)(4)(2-bzpy)](2+) Redox potentials, UV-Vis and NMR spectra

A more direct and efficient route to the syntheses of [Ru(NH3)(4)(X-Y)](BF4)(2), where X-Y can be 2-acetylpyridine (2-acpy) or 2-benzoylpyridine (2-bzpy), based on the reactions of [RuCl(NH3)(5)]Cl-2 with these ortho-substituted azines is described. The [Ru(2-acpy)(NH3)(4)](BF4)(2) and [Ru(NH3)(5)(2-bzpy)](BF4)(2) complexes have a molar conductance of 328 and 292 Ohm(-1) cm(2) mol(-1), respectively, corresponding to a 1:2 species in solution. These complexes showed two intense absorption bands around 620-650 and 380 nm, the energies of which are solvent dependent, decreasing with the increase of the Gutman's donor number of the solvent, and were assigned as metal-to-ligand charge transfer (MLCT). The complexes have oxidation potentials (Ru-II/III) of +0.380 V vs. Ag/AgCl (2-acpy) and +0.400 V vs. Ag/AgCl (2-bzpy), and reduction potentials (X-Y0/-) of -1.10 V vs. Ag/AgCl (2-acpy) and -0.950 V vs. Ag/AgCl (2-bzpy) on CF3COOH/NaCF3COO at pH=3.0, scan rate 100 mV s(-1), [Ru]=1.0x10(-3) mol l(-1). Both processes show a coupled chemical reaction. Upon oxidation of the metal center, the MLCT absorption bands are bleached and restored upon subsequent reduction. In order to confirm the structure of the complexes a detailed LH NMR investigation was performed in d(6)-acetone. Further confirmation of the structure was obtained by recording the N-15 NMR spectrum of [Ru(NH3)(4)(2-bzpy)](2+) in d(6)-DMSO using the INEPT pulse sequence improving the sensitivity of N-15 by polarization transfer from the protons to the N-15. The Nuclear Overhauser Effect (NOE) experiments were made qualitatively for [Ru(NH3)(4)(2-acpy)](2+), and showed that H-6 of the pyridine is close to a NH3 proton, which should then be in a cis position, and, hence, confirming that acpy is acting as a bidentate ligand. (C) 1999 Elsevier B.V. Ltd. All rights reserved.

Using an effective surface charge to explain surface potentials of Langmuir monolayers from dialkyldimethylammonium halides with the Gouy-Chapman theory

The use of an effective surface charge density has allowed the Gouy-Chapman (CC) theory to explain surface potential isotherms of Langmuir monolayers of dioctadecyldimethylammonium bromide (DODAB). The effective surface charge density of DODAB monolayer increases with the electronegativity of the counterions in the subphase. The pressure-area isotherms indicate a very condensed monolayer for DODAB spread on an I--containing subphase, which exhibits the lowest surface charge density, whereas the monolayer on a F-containing subphase is extremely expanded owing to the high surface charge density or electrostatic repulsion between headgroups. (C) 2001 Published by Elsevier B.V. B.V.

Mapping deformed hyperbolic potentials into nondeformed ones

In this work we introduce a mapping between the so-called deformed hyperbolic potentials, which are presenting a continuous interest in the last few years, and the corresponding nondeformed ones. As a consequence, we conclude that these deformed potentials do not pertain to a new class of exactly solvable potentials, but to the same one of the corresponding nondeformed ones. Notwithstanding, we can reinterpret this type of deformation as a kind of symmetry of the nondeformed potentials. © 2005 Elsevier B.V. All rights reserved.

A simple analysis of the influence of the solvent-induced electronic polarization on the N-15 magnetic shielding of pyridine in water

Electronic polarization induced by the interaction of a reference molecule with a liquid environment is expected to affect the magnetic shielding constants. Understanding this effect using realistic theoretical models is important for proper use of nuclear magnetic resonance in molecular characterization. In this work, we consider the pyridine molecule in water as a model system to briefly investigate this aspect. Thus, Monte Carlo simulations and quantum mechanics calculations based on the B3LYP/6-311++G (d,p) are used to analyze different aspects of the solvent effects on the N-15 magnetic shielding constant of pyridine in water. This includes in special the geometry relaxation and the electronic polarization of the solute by the solvent. The polarization effect is found to be very important, but, as expected for pyridine, the geometry relaxation contribution is essentially negligible. Using an average electrostatic model of the solvent, the magnetic shielding constant is calculated as -58.7 ppm, in good agreement with the experimental value of -56.3 ppm. The explicit inclusion of hydrogen-bonded water molecules embedded in the electrostatic field of the remaining solvent molecules gives the value of -61.8 ppm.

The collapse of linear polyelectrolyte chains in a poor solvent: When does a collapsing polyelectrolyte collect its counter ions?

The collapse of linear polyelectrolyte chains in a poor solvent: When does a collapsing polyelectrolyte collect its counter ions? The collapse of polyions in a poor solvent is a complex system and is an active research subject in the theoretical polyelectrolyte community. The complexity is due to the subtle interplay between hydrophobic effects, electrostatic interactions, entropy elasticity, intrinsic excluded volume as well as specific counter-ion and co-ion properties. Long range Coulomb forces can obscure single molecule properties. The here presented approach is to use just a small amount of screening salt in combination with a very high sample dilution in order to screen intermolecular interaction whereas keeping intramolecular interaction as much as possible (polyelectrolyte concentration cp ≤ 12 mg/L, salt concentration; Cs = 10^-5 mol/L). This is so far not described in literature. During collapse, the polyion is subject to a drastic change in size along with strong reduction of free counterions in solution. Therefore light scattering was utilized to obtain the size of the polyion whereas a conductivity setup was developed to monitor the proceeding of counterion collection by the polyion. Partially quaternized PVP’s below and above the Manning limit were investigated and compared to the collapse of their uncharged precursor. The collapses were induced by an isorefractive solvent/non-solvent mixture consisting of 1-propanol and 2-pentanone, with nearly constant dielectric constant. The solvent quality for the uncharged polyion could be quantified which, for the first time, allowed the experimental investigation of the effect of electrostatic interaction prior and during polyion collapse. Given that the Manning parameter M for QPVP4.3 is as low as lB / c = 0.6 (lB the Bjerrum length and c the mean contour distance between two charges), no counterion binding should occur. However the Walden product reduces with first addition of non solvent and accelerates when the structural collapse sets in. Since the dielectric constant of the solvent remains virtually constant during the chain collapse, the counterion binding is entirely caused by the reduction in the polyion chain dimension. The collapse is shifted to lower wns with higher degrees of quaternization as the samples QPVP20 and QPVP35 show (M = 2.8 respectively 4.9). The combination of light scattering and conductivity measurement revealed for the first time that polyion chains already collect their counter ions well above the theta-dimension when the dimensions start to shrink. Due to only small amounts of screening salt, strong electrostatic interactions bias dynamic as well as static light scattering measurements. An extended Zimm formula was derived to account for this interaction and to obtain the real chain dimensions. The effective degree of dissociation g could be obtained semi quantitatively using this extrapolated static in combination with conductivity measurements. One can conclude the expansion factor a and the effective degree of ionization of the polyion to be mutually dependent. In the good solvent regime g of QPVP4.3, QPVP20 and QPVP35 exhibited a decreasing value in the order 1 > g4.3 > g20 > g35. The low values of g for QPVP20 and QPVP35 are assumed to be responsible for the prior collapse of the higher quaternized samples. Collapse theory predicts dipole-dipole attraction to increase accordingly and even predicts a collapse in the good solvent regime. This could be exactly observed for the QPVP35 sample. The experimental results were compared to a newly developed theory of uniform spherical collapse induced by concomitant counterion binding developed by M. Muthukumar and A. Kundagrami. The theory agrees qualitatively with the location of the phase boundary as well as the trend of an increasing expansion with an increase of the degree of quaternization. However experimental determined g for the samples QPVP4.3, QPVP20 and QPVP35 decreases linearly with the degree of quaternization whereas this theory predicts an almost constant value.

The theory of electrostatic probes in strong magnetic fields : Thesis submitted to the Faculty of The Graduate School of the University of Colorado for the Degree Doctor of Philosophy Department of Aerospace Engineering Science

A theory is developed of an electrostatic probe in a fully-ionized plasma in the presence of a strong magnetic field. The ratio of electron Larmor radius to probe transverse dimension is assumed to be small. Poisson's equation, together with kinetic equations for ions and electrons are considered. An asymptotic perturbation method of multiple scales is used by considering the characteristic lengths appearing in the problem. The leading behavior of the solution is found. The results obtained appear to apply to weaker fields also, agreeing with the solutions known in the limit of no magnetic field. The range of potentials for wich results are presented is limited. The basic effects produced by the field are a depletion of the plasma near the probe and a non-monotonic potential surrounding the probe. The ion saturation current is not changed but changes appear in both the floating potential Vf and the slope of the current-voltage diagram at Vf. The transition region extends beyond the space potential Vs,at wich point the current is largely reduced. The diagram does not have an exponential form in this region as commonly assumed. There exists saturation in electron collection. The extent to which the plasma is disturbed is determined. A cylindrical probe has no solution because of a logarithmic singularity at infinity. Extensions of the theory are considered.

Electrostatic steering and ionic tethering in enzyme–ligand binding: Insights from simulations

To bind at an enzyme’s active site, a ligand must diffuse or be transported to the enzyme’s surface, and, if the binding site is buried, the ligand must diffuse through the protein to reach it. Although the driving force for ligand binding is often ascribed to the hydrophobic effect, electrostatic interactions also influence the binding process of both charged and nonpolar ligands. First, electrostatic steering of charged substrates into enzyme active sites is discussed. This is of particular relevance for diffusion-influenced enzymes. By comparing the results of Brownian dynamics simulations and electrostatic potential similarity analysis for triose-phosphate isomerases, superoxide dismutases, and β-lactamases from different species, we identify the conserved features responsible for the electrostatic substrate-steering fields. The conserved potentials are localized at the active sites and are the primary determinants of the bimolecular association rates. Then we focus on a more subtle effect, which we will refer to as “ionic tethering.” We explore, by means of molecular and Brownian dynamics simulations and electrostatic continuum calculations, how salt links can act as tethers between structural elements of an enzyme that undergo conformational change upon substrate binding, and thereby regulate or modulate substrate binding. This is illustrated for the lipase and cytochrome P450 enzymes. Ionic tethering can provide a control mechanism for substrate binding that is sensitive to the electrostatic properties of the enzyme’s surroundings even when the substrate is nonpolar.

On the magnitude of the electrostatic contribution to ligand-DNA interactions.

A model based on the nonlinear Poisson-Boltzmann equation is used to study the electrostatic contribution to the binding free energy of a simple intercalating ligand, 3,8-diamino-6-phenylphenanthridine, to DNA. We find that the nonlinear Poisson-Boltzmann model accurately describes both the absolute magnitude of the pKa shift of 3,8-diamino-6-phenylphenanthridine observed upon intercalation and its variation with bulk salt concentration. Since the pKa shift is directly related to the total electrostatic binding free energy of the charged and neutral forms of the ligand, the accuracy of the calculations implies that the electrostatic contributions to binding are accurately predicted as well. Based on our results, we have developed a general physical description of the electrostatic contribution to ligand-DNA binding in which the electrostatic binding free energy is described as a balance between the coulombic attraction of a ligand to DNA and the disruption of solvent upon binding. Long-range coulombic forces associated with highly charged nucleic acids provide a strong driving force for the interaction of cationic ligands with DNA. These favorable electrostatic interactions are, however, largely compensated for by unfavorable changes in the solvation of both the ligand and the DNA upon binding. The formation of a ligand-DNA complex removes both charged and polar groups at the binding interface from pure solvent while it displaces salt from around the nucleic acid. As a result, the total electrostatic binding free energy is quite small. Consequently, nonpolar interactions, such as tight packing and hydrophobic forces, must play a significant role in ligand-DNA stability.

Fluid mechanical and electrostatic study on the osmotic flow through cylindrical pores

When two solutions differing in solute concentration are separated by a porous membrane, the osmotic pressure will generate a net volume flux of the suspending fluid across the membrane; this is termed osmotic flow. We consider the osmotic flow across a membrane with circular cylindrical pores when the solute and the pore walls are electrically charged, and the suspending fluid is an electrolytic solution containing small cations and anions. Under the condition in which the radius of the pores and that of the solute molecules greatly exceed those of the solvent as well as the ions, a fluid mechanical and electrostatic theory is introduced to describe the osmotic flow in the presence of electric charge. The interaction energy, including the electrostatic interaction between the solute and the pore wall, plays a key role in determining the osmotic flow. We examine the electrostatic effect on the osmotic flow and discuss the difference in the interaction energy determined from the nonlinear Poisson-Boltzmann equation and from its linearized equation (the Debye-Hückel equation).

Applications Of Visual Evoked Potentials And Fourier-domain Optical Coherence Tomography In Parkinson's Disease: A Controlled Study.

The goal of this cross-sectional observational study was to quantify the pattern-shift visual evoked potentials (VEP) and the thickness as well as the volume of retinal layers using optical coherence tomography (OCT) across a cohort of Parkinson's disease (PD) patients and age-matched controls. Forty-three PD patients and 38 controls were enrolled. All participants underwent a detailed neurological and ophthalmologic evaluation. Idiopathic PD cases were included. Cases with glaucoma or increased intra-ocular pressure were excluded. Patients were assessed by VEP and high-resolution Fourier-domain OCT, which quantified the inner and outer thicknesses of the retinal layers. VEP latencies and the thicknesses of the retinal layers were the main outcome measures. The mean age, with standard deviation (SD), of the PD patients and controls were 63.1 (7.5) and 62.4 (7.2) years, respectively. The patients were predominantly in the initial Hoehn-Yahr (HY) disease stages (34.8% in stage 1 or 1.5, and 55.8 % in stage 2). The VEP latencies and the thicknesses as well as the volumes of the retinal inner and outer layers of the groups were similar. A negative correlation between the retinal thickness and the age was noted in both groups. The thickness of the retinal nerve fibre layer (RNFL) was 102.7 μm in PD patients vs. 104.2 μm in controls. The thicknesses of retinal layers, VEP, and RNFL of PD patients were similar to those of the controls. Despite the use of a representative cohort of PD patients and high-resolution OCT in this study, further studies are required to establish the validity of using OCT and VEP measurements as the anatomic and functional biomarkers for the evaluation of retinal and visual pathways in PD patients.

Breaking Oil-in-water Emulsions Stabilized By Yeast.

Several biotechnological processes can show an undesirable formation of emulsions making difficult phase separation and product recovery. The breakup of oil-in-water emulsions stabilized by yeast was studied using different physical and chemical methods. These emulsions were composed by deionized water, hexadecane and commercial yeast (Saccharomyces cerevisiae). The stability of the emulsions was evaluated varying the yeast concentration from 7.47 to 22.11% (w/w) and the phases obtained after gravity separation were evaluated on chemical composition, droplet size distribution, rheological behavior and optical microscopy. The cream phase showed kinetic stability attributed to mechanisms as electrostatic repulsion between the droplets, a possible Pickering-type stabilization and the viscoelastic properties of the concentrated emulsion. Oil recovery from cream phase was performed using gravity separation, centrifugation, heating and addition of demulsifier agents (alcohols and magnetic nanoparticles). Long centrifugation time and high centrifugal forces (2h/150,000×g) were necessary to obtain a complete oil recovery. The heat treatment (60°C) was not enough to promote a satisfactory oil separation. Addition of alcohols followed by centrifugation enhanced oil recovery: butanol addition allowed almost complete phase separation of the emulsion while ethanol addition resulted in 84% of oil recovery. Implementation of this method, however, would require additional steps for solvent separation. Addition of charged magnetic nanoparticles was effective by interacting electrostatically with the interface, resulting in emulsion destabilization under a magnetic field. This method reached almost 96% of oil recovery and it was potentially advantageous since no additional steps might be necessary for further purifying the recovered oil.

Three-nucleon potentials

In this work we describe a subtle effect in nuclear physics, associated with three-nucleon forces, which is nevertheless fundamental in the interpretation of experimental results. It is important to notice that three-body effects are of non-pertubative origins, which makes this problem more involving theoretically. The use of Quantum Chromodynamics is fundamental in the understanding of the physics process.

Analyzing the n→π* Electronic Transition of Formaldehyde in Water. A Sequential Monte Carlo/Time-Dependent Density Functional Theory

The n→π* absorption transition of formaldehyde in water is analyzed using combined and sequential classical Monte Carlo (MC) simulations and quantum mechanics (QM) calculations. MC simulations generate the liquid solute-solvent structures for subsequent QM calculations. Using time-dependent density functional theory in a localized set of gaussian basis functions (TD-DFT/6-311++G(d,p)) calculations are made on statistically relevant configurations to obtain the average solvatochromic shift. All results presented here use the electrostatic embedding of the solvent. The statistically converged average result obtained of 2300 cm-1 is compared to previous theoretical results available. Analysis is made of the effective dipole moment of the hydrogen-bonded shell and how it could be held responsible for the polarization of the solvent molecules in the outer solvation shells.