Evaluation of Poisson solvation models using a hybrid explicit/implicit solvent method

Implicit solvent methods have become popular tools in the field of protein dynamics simulations, yet evaluation of their validity has been primarily limited to comparisons with experimental and theoretical data for small molecules. In this paper, we use a recently developed hybrid explicit/implicit solvent methodology to evaluate the accuracy of several Poisson-based implicit solvent models. Specifically, we focus on the calculation of electrostatic solvation free energies of various fixed conformations for two proteins. We show that, among various dielectric boundary definitions, the Lee-Richards molecular surface has the best agreement with hybrid solvent results. Furthermore, certain modifications of the molecular surface Poisson protocol provide varied results. For instance, simple modifications of atomic radii on charged residues generally improve absolute errors but do not significantly reduce relative errors among conformations. On the other hand, using a water-probe radius of 1.0 A, as opposed to the standard value of 1.4 A, to generate the molecular surface, moderately improves both absolute and relative results.     

The physicochemical surface characteristics of Brevibacterium linens

The physicochemical surface characteristics and interfacial behavior of two strains of Brevibacterium linens (BL-MGE and BL-9174), that may enhance cheese flavor, were assessed. Cell surface hydrophobicity was determined by measuring the contact angle of a variety of polar and non-polar wetting agents on lawns of the bacterial cells. The contact angles obtained were used to calculate the cell surface free energy components γ^LW, γ^AB, γ⁺ and γ⁻. The Lifshitz van der Waals component and the Lewis acid-base component were approximately 35 mJ m⁻² and 22 mJ m⁻², respectively, for both strains. Under conditions of physiological pH and low ionic strength, neither strain exhibited affinity for an octyl ligand in hydrophobic interaction chromatography. This occurred despite a favorable free energy of interfacial interaction which was attributable almost entirely to favorable acid-base interactions between cells and octyl-sepharose. The nature of surface functional groups was evaluated using X-ray photoelectron spectroscopy. Excluding H, the mean percentage of atomic fraction for C, O, N and P for BL-MGE was 57.7, 37.8, 3.9 and 0.6%, respectively and 61.0, 31.8, 7.0 and 0.2%, respectively for BL-9174.     

An apparatus for the determination of volatile analytes by stopped-flow injection analysis using an integrated fiber optic detector

A new method for the analysis of volatile analytes using a stopped-flow injection system originating from either a gas or liquid phase has been developed. It uses an integrated fiber optic detector which also serves as a reactor. This system combines the advantages of gas diffusion and stopped-flow, making the overall assay very sensitive. Both gas streams and aqueous solutions containing ammonia were analyzed. The limits of detection are 40 ppb for gas phase analysis and 1.0 ppm for aqueous phase analysis.