Tests of continuum theories as models of ion channels. I. Poisson-Boltzmann theory versus Brownian dynamics

Continuum theories of electrolytes are widely used to describe physical processes in various biological systems. Although these are well-established theories in macroscopic situations, it is not clear from the outset that they should work in small systems whose dimensions are comparable to or smaller than the Debye length. Here, we test the validity of the mean-field approximation in Poisson-Boltzmann theory by comparing its predictions with those of Brownian dynamics simulations. For this purpose we use spherical and cylindrical boundaries and a catenary shape similar to that of the acetylcholine receptor channel. The interior region filled with electrolyte is assumed to have a high dielectric constant, and the exterior region representing protein a low one. Comparisons of the force on a test ion obtained with the two methods show that the shielding effect due to counterions is overestimated in Poisson-Boltzmann theory when the ion is within a Debye length of the boundary. As the ion gets closer to the boundary, the discrepancy in force grows rapidly. The implication for membrane channels, whose radii are typically smaller than the Debye length, is that Poisson-Boltzmann theory cannot be used to obtain reliable estimates of the electrostatic potential energy and force on an ion in the channel environment.     

A new species of Pliopithecus Gervais, 1849 (Primates: Pliopithecidae) from the Middle Miocene (MN8) of Abocador de Can Mata (els Hostalets de Pierola,Catalonia, Spain)

Pliopithecus (Pliopithecus) canmatensis sp. nov. is described from several Late Aragonian localities from Abocador de Can Mata (ACM) in els Hostalets de Pierola (Vallès‐Penedès Basin, Catalonia, Spain), spanning from ～11.7 to 11.6 Ma (C5r.3r subchron), and being correlated to the MN8 (reference locality La Grive L3). The ACM remains display a pliopithecine dental morphology with well‐developed pliopithecine triangles on M/2 and M/3. This, together with other occlusal details, negates an attribution to the subgenus Epipliopithecus. Although slightly smaller, the ACM remains are most similar in size to comparable elements of P. piveteaui and P. antiquus. Several occlusal details (such as the greater development of the buccal cingulid in lower molars) and dental proportions (M/3 much longer than M/2), however, indicate greater similarities with P. antiquus from Sansan and La Grive. The ACM remains, however, differ from P. antiquus in dental proportions as well as occlusal morphology of the lower molars (including the less peripheral position of the protoconid and more medial position of the hypoconulid, the more mesial position of the buccal cuspids as compared to the lingual ones, the narrower but distinct mesial fovea, the higher trigonid, and the more extensive buccal cingulid, among others). These differences justify a taxonomic distinction at the species level of the ACM pliopithecid remains with respect to P. antiquus. Previous pliopithecid findings from the Vallès‐Penedès Basin, previously attributed to P. antiquus, are neither attributable to the latter species nor to the newly erected one. Am J Phys Anthropol, 2010. © 2009 Wiley‐Liss, Inc.     

Profiling of membrane protein variants in a baculovirus system by coupling cell-surface detection with small-scale parallel expression

Production of structure-grade mammalian membrane proteins in substantial quantities has been hindered by a lack of methods for effectively profiling multiple constructs expression in higher eukaryotic systems such as insect or mammalian cells. To address this problem, a specialized small-scale eukaryotic expression platform by Thomson Instrument Company (Vertiga-IM) was developed and used in tandem with a Guava EasyCyte microcapillary 96-well cytometer to monitor cell density and health and evaluate membrane protein expression. Two proof of concept experiments were conducted using the human beta(2)-adrenergic receptor (beta(2)AR) and the gap junction protein connexin26 (Cx26) in a baculovirus expression system. First, cell surface expression was used to assess the expression levels of 14 beta(2)AR truncation variants expressed using the Vertiga-IM shaker. Three of these variants were then compared to wild-type beta(2)AR using three metrics: cell surface expression, saturation ligand binding and protein immunoblot analysis of dodecylmaltoside extracted material. Second, a series of systematic Cx26 truncation variants were evaluated for expression by protein immunoblot analysis. The cumulative results for these two systems show that the Vertiga-IM instrument can be used effectively in the parallel insect cell microexpression of membrane protein variants, and that the expression of cell surface molecules as monitored with the Guava EasyCyte instrument can be used to rapidly assess the production of properly folded proteins in the baculovirus expression system. This approach expedites the in vitro evaluation of a large number of mammalian membrane protein variants.     

Rapid cultivation of stable aerobic phenol-degrading granules using acetate-fed granules as microbial seed

cDNA-encoding pyranose 2-oxidase (P2O) from Trametes pubescens was sequenced and cloned into Escherichia coli strain BL21/DE3 on a multicopy plasmid under the control of trc promoter. The synthesis of P2O was studied in a batch culture in M9-based mineral medium: the enzyme was synthesized constitutively at 28 °C in amount corresponding to 8% of the cell soluble protein (0.6 U mg⁻¹). Only small portion of P2O (11%) was in the form of non-active inclusion bodies. Purified recombinant enzyme has similar physico-chemical and kinetic parameters with other P2Os. When compared to the expression of p2o of Trametes ochracea, a ratio of the mature enzyme to inclusion bodies found in the same E. coli host at 28 °C is as much as nine times higher. The finding makes the enzyme from T. pubescens preferable for the large-scale production by recombinant bacteria. The difference in amino acid sequences of the P2O from T. ochracea and T. pubescens may explain the favourable trait of the latter enzyme regarding protein folding.     

Towards miniaturization of a structural genomics pipeline using micro-expression and microcoil NMR

In structural genomics centers, nuclear magnetic resonance (NMR) screening is in increasing use as a tool to identify folded proteins that are promising targets for three-dimensional structure determination by X-ray crystallography or NMR spectroscopy. The use of 1D ¹H NMR spectra or 2D [¹H,¹⁵N]-correlation spectroscopy (COSY) typically requires milligram quantities of unlabeled or isotope-labeled protein, respectively. Here, we outline ways towards miniaturization of a structural genomics pipeline with NMR screening for folded globular proteins, using a high-density micro-fermentation device and a microcoil NMR probe. The proteins are micro-expressed in unlabeled or isotope-labeled media, purified, and then subjected to 1D ¹H NMR and/or 2D [¹H,¹⁵N]-COSY screening. To demonstrate that the miniaturization is functioning effectively, we processed nine mouse homologue protein targets and compared the results with those from the “macro-scale” Joint Center of Structural Genomics (JCSG) high-throughput pipeline. The results from the two pipelines were comparable, illustrating that the data were not compromised in the miniaturized approach.