Implicit solvent simulations of DPC micelle formation

The formation of micelles by dodecylphosphocholine (DPC) is modeled by treating the surfactants in atomic detail and the solvent implicitly, in the spirit of the EEF1 solvation model for proteins. The solvation parameters of the DPC atoms are carried over from those of similar atoms in proteins. A slight adjustment of the parameters for the headgroup was found necessary for obtaining an aggregation number consistent with experiment. Molecular dynamics simulations of 960 DPC molecules at different concentrations are used to obtain the aggregation number, the micelle size distribution, and the CMC. At 20 mM concentration we obtain an aggregation number of 53-56 and a CMC of 1.25 mM, values close to the experimental ones. At 100 mM the aggregation number increases to 90. Simulations of individual micelles of varying size show that the effective energy per surfactant molecule is initially a decreasing function of aggregation number but stabilizes at about 60 molecules. The van der Waals term and the desolvation of nonpolar groups contribute to micellization, whereas the desolvation of polar groups opposes it. From the difference between the effective energy and the free energy (calculated from the CMC), the translational and rotational entropy contributions to the free energy are estimated at about 7 kcal/mol per monomer. The micelles obtained here are more irregular than those obtained in explicit water simulations. This modeling approach allows the study of larger surfactant aggregates for longer times and the extraction of thermodynamic in addition to structural information.     

Membrane protein native state discrimination by implicit membrane models

Four implicit membrane models [IMM1, generalized Born (GB)‐surface area‐implicit membrane (GBSAIM), GB with a simple switching (GBSW), and heterogeneous dielectric GB (HDGB)] were tested for their ability to discriminate the native conformation of five membrane proteins from 450 decoys generated by the Rosetta‐Membrane program. The energy ranking of the native state and Z‐scores were used to assess the performance of the models. The effect of membrane thickness was examined and was found to be substantial. Quite satisfactory discrimination was achieved with the all‐atom IMM1 and GBSW models at 25.4 Å thickness and with the HDGB model at 28.5 Å thickness. The energy components by themselves were not discriminative. Both van der Waals and electrostatic interactions contributed to native state discrimination, to a different extent in each model. Computational efficiency of the models decreased in the order: extended‐atom IMM1 > all‐atom IMM1 > GBSAIM > GBSW > HDGB. These results encourage the further development and use of implicit membrane models for membrane protein structure prediction. © 2012 Wiley Periodicals, Inc.     

Menshov’s “adjustment theorem” with respect to general measures

We prove Menshov’s theorem in the setting of arbitrary Borel measures.     

A Characterization of Vanishing Mean Oscillation

We show that a function has vanishing mean oscillation with respect to a nonatomic measure if and only if it satisfies an asymptotic reverse Jensen inequality.     

Calculations of pH-dependent binding of proteins to biological membranes

Binding of proteins to membranes is often accompanied by titration of ionizable residues and is, therefore, dependent on pH. We present a theoretical treatment and computational approach for predicting absolute, pH-dependent membrane binding free energies. The standard free energy of binding, DeltaG, is defined as -RTln(P(b)/P(f)), where P(b) and P(f) are the amounts of bound and free protein. The apparent pK(a) of binding is the pH value at which P(b) and P(f) are equal. Proteins bind to the membrane in the pH range where DeltaG is negative. The components of the binding free energy are (a) the free energy cost of ionization state changes (DeltaG(ion)), (b) the effective energy of transfer from solvent to the membrane surface, (c) the translational/rotational entropy cost of binding, and (d) an ideal entropy term that depends on the relative volume of the bound and free state and therefore depends on lipid concentration. Calculation of the first term requires determination of pK(a) values in solvent and on the membrane surface. All energies required by the method are obtained from molecular dynamics trajectories on an implicit membrane (IMM1-GC). The method is tested on pentalysine and the helical peptide VEEKS, derived from the membrane-binding domain of phosphocholine cytidylyltransferase. The agreement between the measured and the calculated free energies of binding of pentalysine is good. The extent of membrane binding of VEEKS is, however, underestimated compared to experiment. Calculations of the interaction energy between two VEEKS helices on the membrane suggest that the discrepancy is mainly due to the neglect of protein-protein interactions on the membrane surface.     

Exact solutions for linear propagation of chirped pulses using a chirped Gauss Hermite orthogonal basis

A generalized solution of the linear propagation equation is proposed in terms of chirped Gauss-Hermite orthogonal functions. Some well-known special cases are pointed out, and the usefulness of this approach in analyzing arbitrarily shaped chirped pulses in rapidly converging series is discussed.     

Water at biomolecular binding interfaces

Water molecules are often found at the binding interface of biomolecular complexes mediating the interaction between polar groups via hydrogen bonds, or simply filling space providing van der Waals interactions. Recent studies have demonstrated the importance of taking such water molecules into account in docking and binding affinity prediction. Here, we review the recent experimental and theoretical work aimed at quantifying the influence of interfacial water on the thermodynamic properties of binding. We highlight especially our recent results obtained by inhomogeneous fluid solvation theory in several systems and the prediction of the thermodynamic consequences of displacement of the bound water molecule by ligand modification. Finally, we discuss possible directions for further progress in this field.     

Coagulation of Charged Aerosols

We consider the coagulation of an aerosol embedded in a stationary atmosphere of bipolar ions. Particles respond to the ionic environment by developing an instantaneous charge the fluctuations of which may produce attraction or repulsion between the particles. The governing parameter is the charge asymmetry factor which quantifies the relative charging efficiency of positive and negative ions. We use a Monte Carlo method to solve the coagulation equation in the free-molecule regime. We perform simulations for conditions ranging from symmetric and nearly symmetric environments (e.g. flames, ionizers), which result in particles that are on the average neutral to highly asymmetric conditions (low-pressure plasmas), which produce a substantial non-zero net charge. In symmetric ionic atmospheres we find that electrostatic interactions are unimportant and particles grow as if in the absence of charging ions. In asymmetric bipolar atmospheres, electrostatic interactions between particles are repulsive, the mean particle size grows logarithmically in time and the resulting size distributions are significantly narrower than the classical self preserving distributions.     

Comparison of a Rapid Light-Induced and Forced Test to Study the Oxidative Stability of White Wines

The oxidation processes of white wines can occur during storage and commercialization due to several factors, and these can negatively affect the color, aroma, and quality of the wine. Wineries should have faster and simpler methods that provide valuable information on oxidation stability of wines and allow fast decision-making procedures, able to trigger suitable technological interventions. Using a portable prototype instrument for light irradiations at different wavelengths and times was considered and evaluated on sensorial, spectrophotometric, and colorimetric parameters of white wines. The sensorial analysis revealed that white and light blue were the most significant, after only 1 h of irradiation. The experimental results showed that hydrogen peroxide could enhance the effect of light treatment, allowing a contemporary evaluation of the oxidation stability of wine against light and chemical stresses. As expected, a good correlation (R² > 0.89) between optical density at 420 nm and b* parameter was highlighted. The synergic effect of light and H₂O₂ was also studied on the hydrolyzable and condensed tannins’ additions to white wine. The proposed methodology could be used to evaluate the oxidative stability of white wines, but also to evaluate the effect of some oenological adjuvants on wine stability.