A Multi-Scale Approach to Model K+ Permeation Through the KcsA Channel.

K+ channels allow a very efficient passage of K+ ions through the membrane while excluding Na+ ions, and these properties are essential for life. The 3D structure of the KcsA K+ channel, solved more than 20 years ago, allows to address many relevant aspects of K+ permeation and selectivity mechanisms at the molecular level. Recent crystallographic data and molecular dynamics (MD) studies suggest that no water is normally present inside the selectivity filter (SF), which can instead accommodate four adjacent K+ ions. Using a multi-scale approach, whereby information taken from a low-level simulation approach is used to feed a high-level model, we studied the mechanism of K+ permeation through KcsA channels. More specifically, we used MD to find stable ion configurations under physiological conditions. They were characterized by two adjacent K+ ions occupying the more central positions of the SF (sites S2 and S3), while the other two K+ ions could be found at the external and internal entrances to the SF. Sites S1 and S4 were instead not occupied by K+. A continuum Bikerman-Poisson-Boltzmann model that takes into account the volume of the ions and their dehydration when entering the SF fully confirmed the MD results, showing peaks of K+ occupancy at S2, S3, and the external and internal entrances, with S1 and S4 sites being virtually never occupied by K+. Inspired by the newly found ion configuration in the SF at equilibrium, we developed a simple kinetic permeation model which, fed with kinetic rate constants assessed from molecular meta-dynamics, reproduced the main permeation properties of the KcsA channel found experimentally, including sublinear current-voltage and saturating conductance-concentration relationships. This good agreement with the experimental data also implies that the ion configuration in the SF we identified at equilibrium would also be a key configuration during permeation.

Turbulence in a matter-wave supersolid.

Quantum turbulence associated with wave and vortex dynamics is numerically investigated for a two-dimensional trapped atomic Rydberg-dressed Bose-Einstein condensate (BEC). When the coupling constant of the soft-core interaction is over a critical value, the superfluid (SF) system can transition into a hexagonal supersolid (SS) state. Based on the Gross-Pitaevskii equation approach, we have discovered a new characteristic k-13/3 scaling law for wave turbulence in the SS state, that coexists with the waveaction k-1/3 and energy k-1 cascades commonly existing in a SF BEC. The new k-13/3 scaling law implies that the SS system exhibits a negative, minus-one power energy dispersion (E ~ k-1) at the wavevector consistent with the radius of the SS droplet. For vortex turbulence, in addition to the presence of the Kolmogorov energy k-5/3 and Saffman enstrophy k-4 cascades, it is found that large amount of independent vortices and antivortices pinned to the interior of the oscillating SS results in a strong k-1 scaling at the wavevector consistent with the SS lattice constant.

Undular bore theory for the Gardner equation.

We develop modulation theory for undular bores (dispersive shock waves) in the framework of the Gardner, or extended Korteweg-de Vries (KdV), equation, which is a generic mathematical model for weakly nonlinear and weakly dispersive wave propagation, when effects of higher order nonlinearity become important. Using a reduced version of the finite-gap integration method we derive the Gardner-Whitham modulation system in a Riemann invariant form and show that it can be mapped onto the well-known modulation system for the Korteweg-de Vries equation. The transformation between the two counterpart modulation systems is, however, not invertible. As a result, the study of the resolution of an initial discontinuity for the Gardner equation reveals a rich phenomenology of solutions which, along with the KdV-type simple undular bores, include nonlinear trigonometric bores, solibores, rarefaction waves, and composite solutions representing various combinations of the above structures. We construct full parametric maps of such solutions for both signs of the cubic nonlinear term in the Gardner equation. Our classification is supported by numerical simulations.

Synthesis of Pt doped Bi2O3/RuO2 photocatalysts for hydrogen production from water splitting using visible light.

This study was focused on the preparation of modified bismuth oxide photocatalysts, including Ru and Pt doped Bi2O3, using sonochemically assisted method to enhance their photocatalytic activity. The crystalline phase composition and surface structure of Bi2O3 photocatalysts were examined using SEM, XRD, UV-visible spectroscopy, and XPS. Optical characterizations have indicated that the Bi2O3 presents the photoabsorption properties shifting from UV light region into visible light which is approaching towards the edge of 470 nm. According to the experimental results, visible-light-driven photocatalysis for water splitting with the addition of 0.3 M Na2SO3 and 0.03 M H2C2O4 as sacrificing agents demonstrates that Pt/Bi2O3-RuO2 catalyst could increase the amount of hydrogen evolution, which is around 11.6 and 14.5 micromol g(-1) h(-1), respectively. Plausible formation mechanisms of modified bismuth oxide and reaction mechanisms of photocatalytic water splitting have been proposed.

Priming of memory but not effector CD8 T cells by a killed bacterial vaccine.

Killed or inactivated vaccines targeting intracellular bacterial and protozoal pathogens are notoriously ineffective at generating protective immunity. For example, vaccination with heat-killed Listeria monocytogenes (HKLM) is not protective, although infection with live L. monocytogenes induces long-lived, CD8 T cell-mediated immunity. We demonstrate that HKLM immunization primes memory CD8 T lymphocyte populations that, although substantial in size, are ineffective at providing protection from subsequent L. monocytogenes infection. In contrast to live infection, which elicits large numbers of effector CD8 T cells, HKLM immunization primes T lymphocytes that do not acquire effector functions. Our studies show that it is possible to dissociate T cell-dependent protective immunity from memory T cell expansion, and that generation of effector T cells may be necessary for long-term protective immunity.

Drosophila MyD88 is an adapter in the Toll signaling pathway.

Toll-like receptors comprise a family of cell surface receptors that play a crucial role in the innate immune recognition of both Drosophila and mammals. Previous studies have shown that Drosophila Toll-1 mediates the induction of antifungal peptides during fungal infection of adult flies. Through genetic studies, Tube, Pelle, Cactus, and Dif have been identified as downstream components of the Toll-1 signaling pathway. Here we report characterization of a Drosophila homologue of human MyD88, dMyD88. We show that dMyD88 is an adapter in the Toll signaling pathway that associates with both the Toll receptor and the downstream kinase Pelle. Expression of dMyD88 in S2 cells strongly induced activity of a Drosomycin reporter gene, whereas a dominant-negative version of dMyD88 potently inhibited Toll-mediated signaling. We also show that dMyD88 associates with the death domain-containing adapter Drosophila Fas-associated death domain-containing protein (dFADD), which in turn interacts with the apical caspase Dredd. This pathway links a cell surface receptor to an apical caspase in invertebrate cells and therefore suggests that the Toll-mediated pathway of caspase activation may be the evolutionary ancestor of the death receptor-mediated pathway for apoptosis induction in mammals.

TIRAP: an adapter molecule in the Toll signaling pathway.

Mammalian Toll-like receptors (TLRs) recognize conserved products of microbial metabolism and activate NF-kappa B and other signaling pathways through the adapter protein MyD88. Although some cellular responses are completely abolished in MyD88-deficient mice, TLR4, but not TLR9, can activate NF-kappa B and mitogen-activated protein kinases and induce dendritic cell maturation in the absence of MyD88. These differences suggest that another adapter must exist that can mediate MyD88-independent signaling in response to TLR4 ligation. We have identified and characterized a Toll-interleukin 1 receptor (TIR) domain-containing adapter protein (TIRAP) and have shown that it controls activation of MyD88-independent signaling pathways downstream of TLR4. We have also shown that the double-stranded RNA-binding protein kinase PKR is a component of both the TIRAP- and MyD88-dependent signaling pathways.

Structural basis for signal transduction by the Toll/interleukin-1 receptor domains.

Toll-like receptors (TLRs) and the interleukin-1 receptor superfamily (IL-1Rs) are integral to both innate and adaptive immunity for host defence. These receptors share a conserved cytoplasmic domain, known as the TIR domain. A single-point mutation in the TIR domain of murine TLR4 (Pro712His, the Lps(d) mutation) abolishes the host immune response to lipopolysaccharide (LPS), and mutation of the equivalent residue in TLR2, Pro681His, disrupts signal transduction in response to stimulation by yeast and gram-positive bacteria. Here we report the crystal structures of the TIR domains of human TLR1 and TLR2 and of the Pro681His mutant of TLR2. The structures have a large conserved surface patch that also contains the site of the Lps(d) mutation. Mutagenesis and functional studies confirm that residues in this surface patch are crucial for receptor signalling. The Lps(d) mutation does not disturb the structure of the TIR domain itself. Instead, structural and functional studies indicate that the conserved surface patch may mediate interactions with the down-stream MyD88 adapter molecule, and that the Lps(d) mutation may abolish receptor signalling by disrupting this recruitment.

Differences that matter: major cytotoxic T cell-stimulating minor histocompatibility antigens.

Despite thousands of genetic polymorphisms among MHC matched mouse strains, a few unknown histocompatibility antigens are targeted by the cytotoxic T cells specific for tissue grafts. We isolated the cDNA of a novel BALB.B antigen gene that defines the polymorphic H28 locus on chromosome 3 and yields the naturally processed ILENFPRL (IFL8) peptide for presentation by Kb MHC to C57BI/6 CTL. The CTL specific for the IFL8/Kb and our previously identified H60/Kb complexes represent a major fraction of the B6 anti-BALB.B immune response. The immunodominance of these antigens can be explained by their differential transcription in the donor versus the host strains and their expression in professional donor antigen-presenting cells.

Presentation of out-of-frame peptide/MHC class I complexes by a novel translation initiation mechanism.

Immune surveillance by CD8 T cells requires that peptides derived from intracellular proteins be presented by MHC class I molecules on the target cell surface. Interestingly, MHC molecules can also present peptides encoded in alternate translational reading frames, some even without conventional AUG initiation codons. Using T cells to measure expression of MHC bound peptides, we identified the non-AUG translation initiation codons and established that their activity was at the level of translational rather than DNA replication or transcription mechanisms. This translation mechanism decoded the CUG initiation codon not as the canonical methionine but as the leucine residue, and its activity was independent of upstream translation initiation events. Naturally processed peptide/MHC complexes can thus arise from "noncoding" mRNAs via a novel translation initiation mechanism.

The molecular and functional characterization of a dominant minor H antigen, H60.

Minor histocompatibility (H) Ags elicit T cell responses and thereby cause chronic graft rejection and graft-vs-host disease among MHC identical individuals. Although numerous independent H loci exist in mice of a given MHC haplotype, certain H Ags dominate the immune response and are thus of considerable conceptual and therapeutic importance. To identify these H Ags and their genes, lacZ-inducible CD8+ T cell hybrids were generated by immunizing C57BL/6 (B6) mice with MHC identical BALB.B spleen cells. The cDNA clones encoding the precursor for the antigenic peptide/Kb MHC class I complex were isolated by expression cloning using the BCZ39.84 T cell as a probe. The cDNAs defined a new H locus (termed H60), located on mouse chromosome 10, and encoded a novel protein that contains the naturally processed octapeptide LTFNYRNL (LYL8) presented by the Kb MHC molecule. Southern blot analysis revealed that the H60 locus was polymorphic among the BALB and the B6 strains. However, none of the H60 transcripts expressed in the donor BALB spleen were detected in the host B6 strain. The expression and immunogenicity of the LYL8/Kb complex in BALB.B and CXB recombinant inbred strains strongly suggested that the H60 locus may account for one of the previously described antigenic activity among these strains. The results establish the source of an immunodominant autosomal minor H Ag that, by its differential transcription in the donor vs the host strains, provides a novel peptide/MHC target for host CD8+ T cells.