We report that the cyanine dye Cy5 and several of its structural relatives are reversibly quenched by the phosphine TCEP (tris(2-carboxyethyl)phosphine). Using Cy5 as a model, we show that the quenching reaction occurs by 1,4-addition of the phosphine to the polymethine bridge of Cy5 to form a covalent adduct. Illumination with ultraviolet light dissociates the adduct and returns the dye to the fluorescent state. We demonstrate that TCEP quenching can be used for superresolution imaging as well as for other applications, such as differentiating between molecules inside and outside the cell.

As an obligatory pathogen, influenza virus co-opts host cell machinery to harbor infection and to produce progeny viruses. In order to characterize the virus-host cell interactions, several genome-wide siRNA screens and proteomic analyses have been performed recently to identify host factors involved in influenza virus infection. CD81 has emerged as one of the top candidates in two siRNA screens and one proteomic study. The exact role played by CD81 in influenza infection, however, has not been elucidated thus far. In this work, we examined the effect of CD81 depletion on the major steps of the influenza infection. We found that CD81 primarily affected virus infection at two stages: viral uncoating during entry and virus budding. CD81 marked a specific endosomal population and about half of the fused influenza virus particles underwent fusion within the CD81-positive endosomes. Depletion of CD81 resulted in a substantial defect in viral fusion and infection. During virus assembly, CD81 was recruited to virus budding site on the plasma membrane, and in particular, to specific sub-viral locations. For spherical and slightly elongated influenza virus, CD81 was localized at both the growing tip and the budding neck of the progeny viruses. CD81 knockdown led to a budding defect and resulted in elongated budding virions with a higher propensity to remain attached to the plasma membrane. Progeny virus production was markedly reduced in CD81-knockdown cells even when the uncoating defect was compensated. In filamentous virus, CD81 was distributed at multiple sites along the viral filament. Taken together, these results demonstrate important roles of CD81 in both entry and budding stages of the influenza infection cycle.

Viral entry encompasses the initial steps of infection starting from virion host cell attachment to viral genome release. Given the dynamic interactions between the virus and the host, many questions related to viral entry can be directly addressed by live cell imaging. Recent advances in fluorescent labeling of viral and cellular components, fluorescence microscopy with high sensitivity and spatiotemporal resolution, and image analysis enabled studies of a broad spectrum across many viral entry steps, including virus-receptor interactions, internalization, intracellular transport, genomic release, nuclear transport, and cell-to-cell transmission. Collectively, these live cell imaging studies have not only enriched our understandings of the viral entry mechanisms, but also provided novel insights into basic cellular biology processes.

As an obligate pathogen, influenza virus requires host cell factors and compartments to mediate productive infection and to produce infectious progeny virus. Recently, several small interfering RNA (siRNA) knockdown screens revealed influenza virus host dependency proteins, all of which identified at least two subunits of the coat protein I (COPI) complex. COPI proteins oligomerize to form coated vesicles that transport contents between the Golgi apparatus and the endoplasmic reticulum, and they have also been reported to mediate endosomal trafficking. However, it remains unclear which steps in the influenza virus infection cycle rely on the COPI complex. Upon systematic dissection of the influenza virus infection cycle, from entry to progeny virion production, we found that prolonged exposure to COPI complex disruption through siRNA depletion resulted in significant defects in virus internalization and trafficking to late endosomes. Acute inhibition of COPI complex recruitment to the Golgi apparatus with pharmacological compounds failed to recapitulate the same entry defects as observed with the COPI-depleted cells but did result in specific decreases in viral membrane protein expression and assembly, leading to defects in progeny virion production. Taken together, our findings suggest that COPI complexes likely function indirectly in influenza virus entry but play direct roles in viral membrane protein expression and assembly.

Although the biological importance of hepatitis B virus X protein (HBX) in the life cycle of hepatitis B virus has been well established, the cellular and molecular basis of its function remains largely undefined. Despite the association of multiple activities with HBX, none of them appear to provide a unifying hypothesis regarding the true biological function of HBX. Identification and characterization of cellular targets of HBX remain an essential goal in the elucidation of the molecular mechanisms of HBX. Using the Saccharomyces cerevisiae two-hybrid system, we have identified and characterized a novel subunit of the proteasome complex (XAPC7) that interacts specifically with HBX. We also showed that HBX binds specifically to XAPC7 in vitro. Mutagenesis studies have defined the domains of interaction to be critical for the function of HBX. Furthermore, overexpression of XAPC7 appeared to activate transcription by itself and antisense expression of XAPC7 was able to block transactivation by HBX. Therefore, the proteasome complex is possibly a functional target of HBX in cells.

dFunctional convergence of CD28 costimulation and TCR signaling is critical to T-cell activation and adaptive immunity. These receptors form complex microscale patterns within the immune synapse, although the impact of this spatial organization on cell signaling remains unclear. We investigate this cross talk using micropatterned surfaces that present ligands to these membrane proteins in order to control the organization of signaling molecules within the cell-substrate interface. While primary human CD4 ؉ T cells were activated by features containing ligands to both CD3 and CD28, this functional convergence was curtailed on surfaces in which engagement of these two systems was separated by micrometer-scale distances. Moreover, phosphorylated Lck was concentrated to regions of CD3 engagement and exhibited a low diffusion rate, suggesting that costimulation is controlled by a balance between the transport of active Lck to CD28 and its deactivation. In support of this model, disruption of the actin cytoskeleton increased Lck mobility and allowed functional T-cell costimulation by spatially separated CD3 and CD28. In primary mouse CD4؉ T cells, a complementary system, reducing the membrane mobility increased the sensitivity to CD3-CD28 separation. These results demonstrate a subcellular reaction-diffusion system that allows cells to sense the microscale organization of the extracellular environment. Spatial organization plays important roles in cell signaling, governing a wide range of functions, including migration, polarization, and morphogenesis. A striking example at subcellular scales has emerged in the immune synapse (IS), a small (ϳ70-m 2 ) area of contact between a lymphocyte and an antigen-presenting cell (APC) which serves as a platform that focuses and modulates cell-cell communication. The archetypal IS formed between a T cell and an APC contains a central supramolecular activation cluster (cSMAC) of T-cell receptor (TCR)-pMHC complexes surrounded by a peripheral supramolecular activation cluster (pSMAC) with LFA-1-ICAM-1 (1-3). The interfaces of different T-cell-APC pairings exhibit variations on this "bullseye" pattern (4-10), and manipulation of IS structure modulates T-cell activation (11-13), suggesting that microscale organization contributes to the language of cell-cell communication. However, the concept that signaling can be modulated at such scales places stringent requirements on the dynamics of intracellular signaling molecules (14-17), and experimental examples of such mechanisms, particularly within the small dimensions of the IS, have been elusive.We focus here on spatially resolved, microscale cell signaling in the context of CD28 costimulation. When bound by CD80 or CD86, typically presented by an APC in conjunction with pMHC, CD28 augments TCR signaling and is essential for full activation of naive T cells. A role of spatial organization in this signaling was established by experiments in which CD28 was engaged outside the IS, a trans-costimulation configuration representing the action...

Molecules associated with the outer surface of living cells exhibit complex, non-Brownian patterns of diffusion. In this report, supported lipid bilayers were patterned with nanoscale barriers to capture key aspects of this anomalous diffusion in a controllable format. First, long-range diffusion coefficients of membrane-associated molecules were significantly reduced by the presence of the barriers, while short-range diffusion was unaffected. Second, this modulation was more pronounced for large molecular complexes than for individual lipids. Surprisingly, the quantitative effect of these barriers on long-range lipid diffusion could be accurately simulated using a simple, continuum-based model of diffusion on a nanostructured surface; we thus describe a metamaterial that captures the properties of the outer membrane of living cells.The outer surface of cells presents a complex, nanostructured, yet fluid environment that controls the movement of signaling proteins. The lateral movement of many membrane biomolecules, including transmembrane or tethered proteins as well as lipids themselves, can be interpreted as being free and isotropic within compartments of the cell membrane measuring tens to hundreds of nanometers in scale [1][2][3][4][5][6] . These compartments are delineated by semipermeable barriers that arise from interactions between the plasma membrane, underlying cytoskeleton, and associated proteins [6][7][8] . Fluctuations in these structures allow biomolecules to occasionally cross between compartments, allowing long-range, but comparatively slow, transport over the cell surface. More formally, transport along the membrane is an anomalous, non-Brownian process that can be characterized by two diffusion coefficients, one that describes short-range motion within an individual compartment and a second, smaller, effective diffusion coefficient that is associated with long-range motion over many barriers. The extent to which these values differ is dependent on the spacing and properties of the barriers as well as the diffusing molecule. Emerging models suggest significant impacts of this behavior on cell signaling 2, 9, 10 , but experimental systems for testing these hypotheses are not widely available. In this report, we capture this anomalous diffusion by nanopatterning supported lipid bilayers with barriers to lipid diffusion using a geometry that captures the semipermeable nature of those posed to be present in living cells. As is posed by models of these interactions, we aim to gain control over long-range diffusion, while maintaining local, isotropic diffusion associated with a membrane in the absence of such barriers. We demonstrate that these nanopatterned barriers give rise to different short-and long-range diffusion coefficients of lipids and membrane-associated proteins, and provide a quantitative model of this diffusion that suggests specific aspects of membrane structure at the sub-micrometer level. The basic substrate supported lipid bilayer system consists of a phospholipid membrane...

We report here on an approach targeting the host reactive cysteinome to identify inhibitors of host factors required for the infectious cycle of Flaviviruses and other viruses. We used two parallel cellular phenotypic screens to identify a series of covalent inhibitors, exemplified by QL-XII-47, that are active against dengue virus. We show that the compounds effectively block viral protein expression and that this inhibition is associated with repression of downstream processes of the infectious cycle, and thus significantly contributes to the potent antiviral activity of these compounds. We demonstrate that QL-XII-47’s antiviral activity requires selective, covalent modification of a host target by showing that the compound's antiviral activity is recapitulated when cells are preincubated with QL-XII-47 and then washed prior to viral infection and by showing that QL-XII-47R, a non-reactive analog, lacks antiviral activity at concentrations more than 20-fold higher than QL-XII-47's IC90. QL-XII-47’s inhibition of Zika virus, West Nile virus, hepatitis C virus, and poliovirus further suggests that it acts via a target mediating inhibition of these other medically relevant viruses. These results demonstrate the utility of screens targeting the host reactive cysteinome for rapid identification of compounds with potent antiviral activity.