No abstract

h i g h l i g h t s• SDS micelle was simulated for 20 ns using all-atom MD simulation.• SDS conformations are mostly bent in micelle.• Free volume in SDS micelle is ∼0.35% of the micelle volume.• Free energy change for water penetration through SDS micelle is ∼10 kcal/mol.• Dissociation of a single SDS molecule from the micelle requires ∼13 kcal/mol. g r a p h i c a l a b s t r a c t a b s t r a c tWe investigate a micelle consisting of 60 sodium dodecyl sulfate (SDS) molecules in water phase using molecular dynamics simulation method. The dimension of the micelle is evaluated as ∼16Å and ∼21Å for the radius of gyration and geometric radius, respectively, which are well agreed with the previous studies. By calculating the formation energy, it is found that the stability of micelle is driven by the interaction of the micelle with water phase. Via Connolly surface analysis, it was found that ∼58% of the micelle surface is occupied by the hydrophobic alkyl tails. The conformation analysis shows that the individual SDS molecules are bent within the micelle and are not aligned radially from the center-of-mass of the micelle. However, it turns out that the micelle is well packed with a small free volume (0.35% of the micelle volume) which does not allow the diffusion-in of water molecules. The PMF required to drag a water molecule from water phase to the center-of-mass of micelle is calculated as ∼10 kcal/mol while the PMF for a SDS molecule to be dissociated from the micelle is ∼13 kcal/mol, both of which demonstrate that the micellization is driven by minimizing unfavorable interaction of hydrophobic alkyl tail of SDS molecule with water phase.

Lipopolysaccharide (LPS) O-antigen (O-Ag) is known to limit antibody binding to surface antigens, although the relationship between antibody, O-Ag and other outer-membrane antigens is poorly understood. Here we report, immunization with the trimeric porin OmpD from Salmonella Typhimurium (STmOmpD) protects against infection. Atomistic molecular dynamics simulations indicate this is because OmpD trimers generate footprints within the O-Ag layer sufficiently sized for a single IgG Fab to access. While STmOmpD differs from its orthologue in S. Enteritidis (SEn) by a single amino-acid residue, immunization with STmOmpD confers minimal protection to SEn. This is due to the OmpD-O-Ag interplay restricting IgG binding, with the pairing of OmpD with its native O-Ag being essential for optimal protection after immunization. Thus, both the chemical and physical structure of O-Ag are key for the presentation of specific epitopes within proteinaceous surface-antigens. This enhances combinatorial antigenic diversity in Gram-negative bacteria, while reducing associated fitness costs.

Key points A computational model of P2X channel activation in microglia was developed that includes downfield Ca2+‐dependent signalling pathways. This model provides quantitative insights into how diverse signalling pathways in microglia converge to control microglial function. Abstract Microglia function is orchestrated through highly coupled signalling pathways that depend on calcium (Ca2+). In response to extracellular ATP, transient increases in intracellular Ca2+ driven through the activation of purinergic receptors, P2X and P2Y, are sufficient to promote cytokine synthesis. Although the steps comprising the pathways bridging purinergic receptor activation with transcriptional responses have been probed in great detail, a quantitative model for how these steps collectively control cytokine production has not been established. Here we developed a minimal computational model that quantitatively links extracellular stimulation of two prominent ionotropic purinergic receptors, P2X4 and P2X7, with the graded production of a gene product, namely the tumour necrosis factor α (TNFα) cytokine. In addition to Ca2+ handling mechanisms common to eukaryotic cells, our model includes microglia‐specific processes including ATP‐dependent P2X4 and P2X7 activation, activation of nuclear factor of activated T‐cells (NFAT) transcription factors, and TNFα production. Parameters for this model were optimized to reproduce published data for these processes, where available. With this model, we determined the propensity for TNFα production in microglia, subject to a wide range of ATP exposure amplitudes, frequencies and durations that the cells could encounter in vivo. Furthermore, we have investigated the extent to which modulation of the signal transduction pathways influence TNFα production. Our results suggest that pulsatile stimulation of P2X4 via micromolar ATP may be sufficient to promote TNFα production, whereas high‐amplitude ATP exposure is necessary for production via P2X7. Furthermore, under conditions that increase P2X4 expression, for instance, following activation by pathogen‐associated molecular factors, P2X4‐associated TNFα production is greatly enhanced. Given that Ca2+ homeostasis in microglia is profoundly important to its function, this computational model provides a quantitative framework to explore hypotheses pertaining to microglial physiology.

Corneal neovascularization, which occurs in many pathologic states of the cornea, reduces the visual acuity. Recently, we found that the extracellular region of brain-specific angiogenesis inhibitor 1 (BAI1-ECR) has antiproliferative activity through functional blocking of a v b 5 integrin in endothelial cells. In this study, we investigated the effects of lipidmediated subconjunctival injection of the BAI1-ECR gene on corneal angiogenesis induced by epithelial debridement by heptanol in the rabbit. When a pEGFP-BAI1-ECR plasmid was given subconjunctivally 1 week after epithelial debridement, green fluorescence was detected in the corneal stroma with expression persisting for 7 days. To test the effect of BAI1-ECR on neovascularization, rabbits were injected with the BAI1-ECR gene or empty vector two or three times at 1-week intervals beginning 1 week after debridement. When measured with biomicroscopy at 1 or 2 weeks after two weekly injections, BAI1-delivered eyes had significantly less neovascularized corneal area than vector-injected ones in both time periods. Similar microscopic results were obtained after three weekly injections of BAI1-ECR. In quantitative histological examination, the BAI1-receiving eyes showed significantly less neovascular area and number of vessels than vector-injected ones. Also, after two weekly injections, BAI1-delivered eyes had decreased neovascularized corneal area equivalent to that of anti-VEGF antibody-injected ones. These results indicate that BAI1-ECR gene delivery effectively reduces experimental corneal neovascularization and suggest that the BAI1-ECR protein can be used as an angiogenesis suppressor in the eye. Gene Therapy (2005) 12, 617-624.