Architecture of the bacteriophage lambda tail.

Bacteriophage lambda has a double-stranded DNA genome and a long, flexible, non-contractile tail encoded by a contiguous block of 11 genes downstream of the head genes. The tail allows host recognition and delivery of viral DNA from the head shell to the cytoplasm of the infected cell. Here, we present a high-resolution structure of the tail complex of bacteriophage lambda determined by cryoelectron microscopy.

Structural Basis of the Mechanisms of Action and Immunity of Lactococcin A, a Class IId Bacteriocin.

Lactococcin A (LcnA), a class IId bacteriocin, induces membrane leakage and cell death by specifically binding to the membrane receptor-mannose phosphotransferase system (man-PTS), as is the case for pediocin-like (class IIa) bacteriocins. The cognate immunity protein of bacteriocins, which protects the producer cell from its own bacteriocin, recognizes and binds to the bacteriocin-man-PTS complex, consequently blocking membrane leakage. We previously deciphered the mode of action and immunity of class IIa bacteriocins.

A novel serum spherical lectin from lamprey reveals a more efficient mechanism of immune initiation and regulation in jawless vertebrates.

The innate immune system is the body's first line of defense against pathogens and involves antibody and complement system-mediated antigen removal. Immune-response-related complement molecules have been identified in lamprey, and the occurrence of innate immune response via the mannose-binding lectin-associated serine proteases of the lectin cascade has been reported. We have previously shown that lamprey (Lampetra japonica) serum can efficiently and specifically eliminate foreign pathogens.

Nicking mechanism underlying the DNA phosphorothioate-sensing antiphage defense by SspE.

DNA phosphorothioate (PT) modification, with a nonbridging phosphate oxygen substituted by sulfur, represents a widespread epigenetic marker in prokaryotes and provides protection against genetic parasites. In the PT-based defense system Ssp, SspABCD confers a single-stranded PT modification of host DNA in the 5'-CCA-3' motif and SspE impedes phage propagation. SspE relies on PT modification in host DNA to exert antiphage activity.

The crystal structure of Atg18 reveals a new binding site for Atg2 in Saccharomyces cerevisiae.

Macroautophagy (hereafter referred to as autophagy) is a highly conserved catabolic eukaryotic pathway that is critical for stress responses and homeostasis. Atg18, one of the core proteins involved in autophagy, belongs to the PROPPIN family and is composed of seven WD40 repeats. Together with Atg2, Atg18 participates in the elongation of phagophores and the recycling of Atg9 in yeast.

Structural and functional insight into the effect of AFF4 dimerization on activation of HIV-1 proviral transcription.

Super elongation complex (SEC) is a positive regulator of RNA polymerase II, which is required for HIV-1 proviral transcription. AFF1/4 is the scaffold protein that recruits other components of SEC and forms dimer depending on its THD domain (TPRL with Handle Region Dimerization Domain). Here we report the crystal structure of the human AFF4-THD at the resolution of 2.

Inward-facing conformation of l-ascorbate transporter suggests an elevator mechanism.

Various bacteria can ferment vitamin C (l-ascorbate) under anaerobic conditions via the phosphoenolpyruvate-dependent phosphotransferase system (PTS). The PTS system is composed of two soluble energy-coupling proteins (EI and HPr) and an enzyme II complex (EIIA, EIIB, and EIIC) for the anaerobic uptake of ascorbate and its phosphorylation to l-ascorbate 6-phosphate in vivo. Crystal structures of the ascorbate-bound EIIC component from are available in outward-open and occluded conformations, suggesting a possible elevator mechanism of membrane transport.

Gold nanocage assemblies for selective second harmonic generation imaging of cancer cell.

Second harmonic generation (SHG) imaging using near infrared laser light is the key to improving penetration depths, leading to biological understanding. Unfortunately, currently SHG imaging techniques have limited capability due to the poor signal-to-noise ratio, resulting from the low SHG efficiency of available dyes. Targeted tumor imaging over nontargeted tissues is also a challenge that needs to be overcome.

Plasmon-induced transparency in the visible region via self-assembled gold nanorod heterodimers.

The phenomenon of plasmon-induced transparency holds immense potential for high sensitivity sensors and optical information processing due to the extreme dispersion and slowing of light within a narrow spectral window. Unfortunately plasmonic metamaterials demonstrating this effect has been restricted to infrared and greater wavelengths due to requisite precision in structure fabrication. Here we report a novel metamaterial synthesized by bottom-up self-assembly of gold nanorods.

Plasmonic resonances in self-assembled reduced symmetry gold nanorod structures.

Self-assembled plasmonic Dolmen structures consisting of small gold nanorods (length = 50 nm and diameter = 20 nm) with a few nanometer gaps are observed to show coherent effects of super-radiance and characteristics of Fano resonance due to the significantly reduced symmetry of the structure. Relative to previous larger structures from top-down electron-beam lithography, the single crystallinity and atomically smooth surfaces of these self-assembled plasmonic structures result in 50% narrower resonances, and the small gaps with associated strong coupling enable observation of multiple dark and bright modes. By tilting the cap monomer with respect to the base dimer an order of magnitude increase in E-field enhancement at the Fano dip is obtained.

Pronounced effects of anisotropy on plasmonic properties of nanorings fabricated by electron beam lithography.

Gold nanoring dimers were fabricated via EBL with dimensions of 127.6 ± 2.5 and 57.

Computational model of hepatitis B virus DNA polymerase: molecular dynamics and docking to understand resistant mutations.

Hepatitis B virus (HBV) DNA polymerase (HDP) is a pharmacological target of intense interest. Of the seven agents approved in USA for the treatment of HBV infections, five are HDP inhibitors. However, resistance development against HDP inhibitors, such as lamivudine and adefovir, has severely hurt their efficacy to treat HBV.

Solvation in supercritical water.

Solvation in supercritical water under equilibrium and nonequilibrium conditions is studied via molecular dynamics simulations. The influence of solute charge distributions and solvent density on the solvation structures and dynamics is examined with a diatomic probe solute molecule. It is found that the solvation structure varies dramatically with the solute dipole moment, especially in low-density water, in accord with many previous studies on ion solvation.