Influenza virus presents a significant and persistent threat to public health worldwide and current vaccines provide immunity to viral isolates similar to the vaccine strain. High affinity antibodies against a conserved epitope could provide immunity to the diverse influenza subtypes and protection against future pandemic viruses. Co-crystal structures were determined at 2.2 and 2.7 Å resolutions for broadly neutralizing human antibody CR6261 Fab in complexes with the major surface antigen (hemagglutinin, HA) from viruses responsible for the 1918 H1N1 influenza pandemic and a recent lethal case of H5N1 avian influenza. In contrast to all other structurally characterized influenza antibodies, CR6261 recognizes a highly conserved helical region in the membrane-proximal stem of HA1/HA2. The antibody neutralizes the virus by blocking conformational rearrangements associated with membrane fusion. The CR6261 epitope identified here should accelerate the design and implementation of improved vaccines that can elicit CR6261-like antibodies, as well as antibodybased therapies for the treatment of influenza.Over the past century, three human influenza A pandemics (1918 H1N1 Spanish, 1957 H2N2 Asian, and 1968 have killed ∼50-100 million people worldwide. Each pandemic virus was derived, at least in part, from an avian influenza virus by direct interspecies transmission or exchange of genetic material between avian and human viruses (1-4). In each case, a novel hemagglutinin (HA) envelope glycoprotein was acquired that was antigenically distinct from the HAs of the human viruses in circulation at that time. HA is the primary target of neutralizing antibodies and rapidly and continuously accumulates mutations to escape recognition by the immune system. In pandemic years, HAs are shuffled from the vast reservoir of 16 HA subtypes in avian viruses into a circulating human virus to evade prevailing immunity in the human population. Thus, while many factors likely contribute to virulence and transmissibility, immune evasion is critical for the rapid spread of pandemic and epidemic viruses.Several small molecules are in use for treatment of influenza. Most notable are neuraminidase (NA) inhibitors, oseltamivir (Tamiflu) and zanamivir (Relenza), that prevent release of nascent virions, and amantadine (5) that interferes with the M2 channel proton conducting activity. However, excessive use leads to resistant viruses (6-8) that often show surprisingly little attenuation from the escape mutations, thereby contributing to rapid spread worldwide (6).

The observed red shift of the T203Y YFP variant is proposed to be mainly due to the additional polarizability of the pi-stacked Tyr203. The altered location of the chromophore suggests that the exact positions of nearby residues are not crucial for the chemistry of chromophore formation. The YFPs significantly extend the pH range over which GFPs may be employed as pH indicators in live cells.

The green fluorescent protein (GFP) from the jellyfish Aequorea victoria has become a useful tool in molecular and cell biology. Recently, it has been found that the fluorescence spectra of most mutants of GFP respond rapidly and reversibly to pH variations, making them useful as probes of intracellular pH. To explore the structural basis for the titration behavior of the popular GFP S65T variant, we determined high-resolution crystal structures at pH 8.0 and 4.6. The structures revealed changes in the hydrogen bond pattern with the chromophore, suggesting that the pH sensitivity derives from protonation of the chromophore phenolate. Mutations were designed in yellow fluorescent protein (S65G/V68L/S72A/T203Y) to change the solvent accessibility (H148G) and to modify polar groups (H148Q, E222Q) near the chromophore. pH titrations of these variants indicate that the chromophore pKa can be modulated over a broad range from 6 to 8, allowing for pH determination from pH 5 to pH 9. Finally, mutagenesis was used to raise the pKa from 6.0 (S65T) to 7.8 (S65T/H148D). Unlike other variants, S65T/H148D exhibits two pH-dependent excitation peaks for green fluorescence with a clean isosbestic point. This raises the interesting possibility of using fluorescence at this isosbestic point as an internal reference. Practical real time in vivo applications in cell and developmental biology are proposed.

Structural genomics is emerging as a principal approach to define protein structure-function relationships. To apply this approach on a genomic scale, novel methods and technologies must be developed to determine large numbers of structures. We describe the design and implementation of a high-throughput structural genomics pipeline and its application to the proteome of the thermophilic bacterium Thermotoga maritima. By using this pipeline, we successfully cloned and attempted expression of 1,376 of the predicted 1,877 genes (73%) and have identified crystallization conditions for 432 proteins, comprising 23% of the T. maritima proteome. Representative structures from TM0423 glycerol dehydrogenase and TM0449 thymidylate synthase-complementing protein are presented as examples of final outputs from the pipeline.

Fifteen rare cancer-derived mutants of PIK3CA, the gene coding for the catalytic subunit p110␣ of phosphatidylinositol 3-kinase (PI3K), were examined for their biological and biochemical properties. Fourteen of these mutants show a gain of function: they induce rapamycin-sensitive oncogenic transformation of chicken embryo fibroblasts, constitutively activate Akt and TOR-mediated signaling, and show enhanced lipid kinase activity. Mapping of these mutants on a partial structural model of p110␣ suggests three groups of mutants, defined by their location in distinct functional domains of the protein. We hypothesize that each of these three groups induces a gain of PI3K function by a different molecular mechanism. Mutants in the C2 domain increase the positive surface charge of this domain and therefore may enhance the recruitment of p110␣ to cellular membranes. Mutants in the helical domain map to a contiguous surface of the protein and may affect the interaction with other protein(s). Mutants in the kinase domain are located near the hinge of the activation loop. They may alter the position and mobility of the activation loop. Arbitrarily introduced mutations that have no detectable phenotype map either to the interior of the protein or are positioned on a surface region that lies opposite to the exposed surfaces containing gain-of-function mutants. Engineered mutants that exchange acidic or neutral residues for basic residues on the critical surfaces show a gain of function. molecular model ͉ phosphatidylinositol 3-kinase ͉ lipid membrane ͉ protein-protein interaction ͉ activation loop T he catalytic subunit p110␣ of class I phosphatidylinositol 3-kinase (PI3K) is frequently mutated in cancer (1-5). The incidence of these cancer-specific point mutations varies with the tissue of origin and is particularly high in mammary and colorectal cancers (1, 2, 6 -12). A conspicuous feature of the p110␣ mutations is their specific location in the gene of p110␣: almost 80% of these mutations map to one of three hot spots in the p110␣ coding sequence (1). Two of the hot spot mutations are located in the helical domain of p110␣ at residue positions E542K and E545K, and the third hot spot (residue H1047R) is located in the C-terminal portion of the kinase domain. Besides these frequently occurring hot spot mutations, numerous rare, cancer-specific mutations have also been identified in p110␣ (1,3,7,8,10,11). These rare mutations are widely distributed over the entire coding sequence of p110␣. It has been assumed that the prevalence of hot spot mutations ref lects the strong selective growth advantage that these mutants provide to the cell. This suggestion is supported by the fact that all three hot spot mutations confer in vitro and in vivo oncogenicity on p110␣ (13-18). A corollary of this interpretation is that the rare mutants would not offer a comparable growth advantage and may therefore show either no phenotype or a loss of function. Consequently, they may be of no relevance to the oncogenic process. We studied 15 of the...

CD1 antigens bind a variety of self and foreign lipid and glycolipid antigens for presentation to CD1-restricted T cell receptors (TCRs). Here we report the crystal structure of human CD1a in complex with a sulfatide self antigen at a resolution of 2.15 A. The lipid adopts an S-shaped conformation, with the sphingosine chain completely buried in the A' pocket and the fatty acid chain emerging from the interface of the A' pocket into the more exposed F' pocket. The headgroup is anchored in the A'-F' junction and protrudes into the F' pocket for TCR recognition. Because the A' pocket is narrow with a fixed terminus, it can act as a molecular 'ruler' to select alkyl chains of a particular length.

Sialidase (neuraminidase, EC 3.2.1.18) catalyses the hydrolysis of terminal sialic acid residues of glyconjugates. Sialidase has been well studied in viruses and bacteria where it destroys the sialic acid-containing receptors at the surface of host cells, and mobilizes bacterial nutrients. In mammals, three types of sialidases, lysosomal, plasma membrane and cytosolic, have been described. For lysosomal sialidase in humans, the primary genetic deficiency results in an autosomal recessive disease, sialidosis, associated with tissue accumulation and urinary excretion of sialylated oligosaccharides and glycolipids. Sialidosis includes two main clinical variants: late-onset, sialidosis type I, characterized by bilateral macular cherry-red spots and myoclonus, and infantile-onset, sialidosis type II, characterized by skeletal dysplasia, mental retardation and hepatosplenomegaly. We report the identification of human lysosomal sialidase cDNA, its cloning, sequencing and expression. Examination of six sialidosis patients revealed three mutations, one frameshift insertion and two missense. We mapped the lysosomal sialidase gene to human chromosome 6 (6p21.3), which is consistent with the previous chromosomal assignment of this gene in proximity to the HLA locus.

Summary Pili are proteinaceous polymers of linked pilins that protrude from the cell surface of many bacteria and often mediate adherence and virulence. We investigated a set of 20 Bacteroidia pilins from the human microbiome whose structures and mechanism of assembly were unknown. Crystal structures and biochemical data revealed a diverse protein superfamily with a common Greek-key β-sandwich fold with two transthyretin-like repeats that polymerize into a pilus through a strand-exchange mechanism. The assembly mechanism of the central, structural pilins involves proteinase-assisted removal of their N-terminal β-strand, creating an extended hydrophobic groove that binds the C-terminal donor strands of the incoming pilin. Accessory pilins at the tip and base have unique structural features specific to their location, allowing initiation or termination of the assembly. The bacteroidia pilus therefore has a biogenesis mechanism that is distinct from other known pili and likely represents a different type of bacterial pilus.