Structure of the dengue virus envelope protein after membrane fusion

Dengue virus enters a host cell when the viral envelope glycoprotein, E, binds to a receptor and responds by conformational rearrangement to the reduced pH of an endosome. The conformational change induces fusion of viral and host-cell membranes. A three-dimensional structure of the soluble E ectodomain (sE) in its trimeric, postfusion state reveals striking differences from the dimeric, prefusion form. The elongated trimer bears three 'fusion loops' at one end, to insert into the host-cell membrane. Their structure allows us to model directly how these fusion loops interact with a lipid bilayer. The protein folds back on itself, directing its carboxy terminus towards the fusion loops. We propose a fusion mechanism driven by essentially irreversible conformational changes in E and facilitated by fusion-loop insertion into the outer bilayer leaflet. Specific features of the folded-back structure suggest strategies for inhibiting flavivirus entry.     

Molecular model for a complete clathrin lattice from electron cryomicroscopy

Clathrin-coated vesicles are important vehicles of membrane traffic in cells. We report the structure of a clathrin lattice at subnanometre resolution, obtained from electron cryomicroscopy of coats assembled in vitro. We trace most of the 1,675-residue clathrin heavy chain by fitting known crystal structures of two segments, and homology models of the rest, into the electron microscopy density map. We also define the position of the central helical segment of the light chain. A helical tripod, the carboxy-terminal parts of three heavy chains, projects inward from the vertex of each three-legged clathrin triskelion, linking that vertex to 'ankles' of triskelions centred two vertices away. Analysis of coats with distinct diameters shows an invariant pattern of contacts in the neighbourhood of each vertex, with more variable interactions along the extended parts of the triskelion 'legs'. These invariant local interactions appear to stabilize the lattice, allowing assembly and uncoating to be controlled by events at a few specific sites.     

X-ray structure of a protein-conducting channel

A conserved heterotrimeric membrane protein complex, the Sec61 or SecY complex, forms a protein-conducting channel, allowing polypeptides to be transferred across or integrated into membranes. We report the crystal structure of the complex from Methanococcus jannaschii at a resolution of 3.2 A. The structure suggests that one copy of the heterotrimer serves as a functional translocation channel. The alpha-subunit has two linked halves, transmembrane segments 1-5 and 6-10, clamped together by the gamma-subunit. A cytoplasmic funnel leading into the channel is plugged by a short helix. Plug displacement can open the channel into an 'hourglass' with a ring of hydrophobic residues at its constriction. This ring may form a seal around the translocating polypeptide, hindering the permeation of other molecules. The structure also suggests mechanisms for signal-sequence recognition and for the lateral exit of transmembrane segments of nascent membrane proteins into lipid, and indicates binding sites for partners that provide the driving force for translocation.     

Linkage disequilibrium of a type 1 diabetes susceptibility locus with a regulatory IL12B allele

Type 1 diabetes (T1D; or insulin-dependent diabetes mellitus, IDDM) is an autoimmune disease with both genetic and environmental components. In addition to the human leukocyte antigen (HLA) complex, the single major genetic contributor of susceptibility, an unknown number of other unidentified genes are required to mediate disease. Although many loci conferring susceptibility to T1D have been mapped, their identification has proven problematic due to the complex nature of this disease. Our strategy for finding T1D susceptibility genes has been to test for human homologues of loci implicated in diabetes-prone NOD (non-obese diabetic) mice, together with application of biologically relevant stratification methods. We report here a new susceptibility locus, IDDM18, located near the interleukin-12 (IL-12)p40 gene, IL12B. Significant bias in transmission of IL12B alleles was observed in affected sibpairs and was confirmed in an independent cohort of simplex families. A single base change in the 3' UTR showed strong linkage disequilibrium with the T1D susceptibility locus. The IL12B 3' UTR alleles showed different levels of expression in cell lines. Variation in IL-12p40 production may influence T-cell responses crucial for either mediating or protecting against this and other autoimmune diseases.     

Variance estimation for multivariate dynamic linear models

The problem of estimating unknown observational variances in multivariate dynamic linear models is considered. Conjugate procedures are possible for univariate models and also for special very restrictive common components models but they are not generally applicable. However, for clarity of operation and in order to avoid numerical integration, it is desirable to have conjugacy or approximate conjugacy. Such an approximate procedure is proposed based upon a simple analytic approximation. It is exact for the sub-class of conjugate models and improves on a previous procedure based upon the Robust filter.     

Discount weighted estimation

The parsimonious method of exponentially weighted regression (EWR) is attractive but limited in application because it depends upon just one discount factor. This paper generalizes the EWR approach to a method called discount weighted estimation (DWE) which allowed distinct model components to have different associated discount factors. The method includes EWR as a special case. The general non-limiting recurrence relationships will be useful in practice, especially when practitioners wish to specify prior information, to intervene with subjective judgement and to derive estimates and forecasts sequentially based upon limited data. Two theorems extend the important EWR limiting results of Dobbie and McKenzie to DWE. The latter permits the derivation of a large class of known processs for which DWE is optimal. The method is illustrated by two applications, one of which uses the famous international airline passenger data. This allows a comparision with the ICI MULDO system which uses a particular two discount factor forecasting method. A companion paper extends the discount methods to Bayesian forecasting, Kalman filtering and state space modelling.     

Fabrication of photonic crystals for the visible spectrum by holographic lithography

The term 'photonics' describes a technology whereby data transmission and processing occurs largely or entirely by means of photons. Photonic crystals are microstructured materials in which the dielectric constant is periodically modulated on a length scale comparable to the desired wavelength of operation. Multiple interference between waves scattered from each unit cell of the structure may open a 'photonic bandgap'--a range of frequencies, analogous to the electronic bandgap of a semiconductor, within which no propagating electromagnetic modes exist. Numerous device principles that exploit this property have been identified. Considerable progress has now been made in constructing two-dimensional structures using conventional lithography, but the fabrication of three-dimensional photonic crystal structures for the visible spectrum remains a considerable challenge. Here we describe a technique--three-dimensional holographic lithography--that is well suited to the production of three-dimensional structures with sub-micrometre periodicity. With this technique we have made microperiodic polymeric structures, and we have used these as templates to create complementary structures with higher refractive-index contrast.     

Structure of the reovirus core at 3.6 A resolution

The reovirus core is an assembly with a relative molecular mass of 52 million that synthesizes, modifies and exports viral messenger RNA. Analysis of its structure by X-ray crystallography shows that there are alternative, specific and completely non-equivalent contacts made by several surfaces of two of its proteins; that the RNA capping and export apparatus is a hollow cylinder, which probably sequesters its substrate to ensure completion of the capping reactions; that the genomic double-stranded RNA is coiled into concentric layers within the particle; and that there is a protein shell that appears to be common to all groups of double-stranded RNA viruses.