Fluorescent proteins as proteomic probes

Protein complexes mediate the majority of cellular processes. Knowledge of the localization and composition of such complexes provides key insights into their functions. Although green fluorescent protein (GFP) has been widely applied for in vivo visualization of proteins, it has been relatively little used as a tool for the isolation of protein complexes. Here we describe the use of the standard GFP tag to both visualize proteins in living cells and capture their interactions via a simple immunoaffinity purification procedure. We applied this method to the analysis of a variety of endogenous protein complexes from different eukaryotic cells. We show that efficient isolations can be achieved in 5-60 min. This rapid purification helps preserve protein complexes close to their original state in the cell and minimizes nonspecific interactions. Given the wide use and availability of GFP-tagged protein reagents, the present method should greatly facilitate the elucidation of many cellular processes.     

Reprogramming cellular functions with engineered membrane proteins

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Emerging non-canonical functions for heterotrimeric G proteins in cellular signaling

Abstract

Classically heterotrimeric G proteins have been described as the principal signal transducing machinery for G-protein-coupled receptors. Receptor activation catalyzes nucleotide exchange on the Gα protein, enabling Gα-GTP and Gβγ-subunits to engage intracellular effectors to generate various cellular effects such as second messenger production or regulation of ion channel conductivity. Recent genetic and proteomic screens have identified novel heterotrimeric G-protein-interacting proteins and expanded their functional roles. This review highlights some examples of recently identified interacting proteins and summarizes how they functionally connect heterotrimeric G proteins to previously underappreciated cellular roles.     

Fluorescent proteins as a toolkit for in vivo imaging

Green fluorescent protein (GFP) from the jellyfish Aequorea victoria, and its mutant variants, are the only fully genetically encoded fluorescent probes available and they have proved to be excellent tools for labeling living specimens. Since 1999, numerous GFP homologues have been discovered in Anthozoa, Hydrozoa and Copepoda species, demonstrating the broad evolutionary and spectral diversity of this protein family. Mutagenic studies gave rise to diversified and optimized variants of fluorescent proteins, which have never been encountered in nature. This article gives an overview of the GFP-like proteins developed to date and their most common applications to study living specimens using fluorescence microscopy.     

Arabidopsis thaliana J-class heat shock proteins: cellular stress sensors

Plants are sessile organisms that have evolved a variety of mechanisms to maintain their cellular homeostasis under stressful environmental conditions. Survival of plants under abiotic stress conditions requires specialized group of heat shock protein machinery, belonging to Hsp70:J-protein family. These heat shock proteins are most ubiquitous types of chaperone machineries involved in diverse cellular processes including protein folding, translocation across cell membranes, and protein degradation. They play a crucial role in maintaining the protein homeostasis by reestablishing functional native conformations under environmental stress conditions, thus providing protection to the cell. J-proteins are co-chaperones of Hsp70 machine, which play a critical role by stimulating Hsp70s ATPase activity, thereby stabilizing its interaction with client proteins. Using genome-wide analysis of Arabidopsis thaliana, here we have outlined identification and systematic classification of J-protein co-chaperones which are key regulators of Hsp70s function. In comparison with Saccharomyces cerevisiae model system, a comprehensive domain structural organization, cellular localization, and functional diversity of A. thaliana J-proteins have also been summarized.     

Fluorescent nanoparticles as selective Cu(II) sensors.

Latex nanoparticles functionalized with cyclam (1,4,8,11-tetraazacyclotetradecane), a copper chelator, have been doped with a fluorescent dye (BODIPY derivative: 4,4-difluoro-8-(2',4',6'-trimethyl)phenyl-2,6-diethyl-1,3,5,7-tetramethyl-4-bora-3a,4a-diaza-s-indacene). The bulky, hydrophobic fluorophore dissolves within the nanoparticles' polymer core up to a concentration of about 88.4 micromol g(-1). At this concentration the fluorescence yield is about 0.80. Adding Cu2+ ions to the solution decreases the fluorescence because of the energy transfer between the dye and the violet copper cyclam complexes. The response is fast: 90% of the quenching occurs within 1 s. The Cu2+ detection threshold is of 1 nanomolar. No interferences were observed with zinc and nickel ions.     

Clustering proteins from interaction networks for the prediction of cellular functions

Background  

Developing reliable and efficient strategies allowing to infer a function to yet uncharacterized proteins based on interaction networks is of crucial interest in the current context of high-throughput data generation. In this paper, we develop a new algorithm for clustering vertices of a protein-protein interaction network using a density function, providing disjoint classes.     

Fluorescent sensors for rapid monitoring of intracellular cGMP

Sensors based on fluorescence resonance energy transfer (FRET) are powerful tools to monitor signaling events in living mammalian cells. Here we describe development and use of new sensors for cyclic GMP (cGMP) based on cGMP binding domains from cGMP-dependent protein kinase I (GKI) and from phosphodiesterases (PDEs). The temporal and spatial resolution attained with the new sensors is superior to that of existing techniques, and permits direct recording and imaging of rapid cGMP-signaling events.     

CD147相互作用蛋白及其细胞生物学功能

CD147（basigin、EMMPRIN、neurothelin、M6、HAb18G等）是一个跨膜糖蛋白家族,广泛表达于各种上皮细胞,但其表达在大鼠、小鼠、鸡和人等不同种属间存在很大差异性。CD147高表达于上皮来源的肿瘤细胞表面,如肺癌、乳腺癌和肝癌等。CD147抗原胞外段有2个IgSF结构域,跨膜区有一个带电谷氨酸（GIu）残基,胞内段含有40个氨基酸。CD147的结构特点提示其可能参与蛋白-蛋白相互作用。由于CD147分子的3D结构信息还没有获得,与其相互作用的分子还没有完全明确,但近来应用黏附、免疫共沉淀等实验方法,一些研究报道提示,CD147可与整合素（integrin）、环亲合素（cyclophilins）、单羧酸转运器（monocarboxylate transporter,MCT）等蛋白相互作用,而这些蛋白可能作为CD147分子的候选配体或受体,通过蛋白-蛋白相互作用,介导广泛的上皮细胞生物学功能。     

Fluorescent dyes as probes to study lipid-binding proteins

We studied the equilibrium binding of two hydrophobic fluorescent dyes, ANS and bisANS, to four members of a family of intracellular lipid-binding proteins: IFABP, CRABP I, CRABP II, and ILBP. The spectral and binding parameters for the probes bound to the proteins were determined. Typically, there was a single binding site on each protein for the ligands. However, IFABP cooperatively bound a second bisANS molecule in the binding pocket. Comparative analysis of affinities and spectral characteristics for the two probes allowed us to examine the contributions of electrostatic and hydrophobic interactions to the binding process, and to address some aspects of the internal structure of the studied proteins.     

Fluorescent proteins as tools to aid protein production

Fluorescent proteins are genetically encoded, highly versatile reporters useful for monitoring various aspects of recombinant protein production. In addition to the widely popular green fluorescent protein (GFP) from Aequorea victoria, a variety of other fluorescent proteins have been discovered that display a wide range of spectral properties. Synthetic variants have also been developed to overcome limitations associated with their wild-type counterparts. Having a large repertoire of fluorescent proteins with diverse traits opens new opportunities for rapid monitoring and optimization of recombinant protein production.     

Dystrophin complex functions as a scaffold for signalling proteins

Dystrophin is a 427 kDa sub-membrane cytoskeletal protein, associated with the inner surface membrane and incorporated in a large macromolecular complex of proteins, the dystrophin-associated protein complex (DAPC). In addition to dystrophin the DAPC is composed of dystroglycans, sarcoglycans, sarcospan, dystrobrevins and syntrophin. This complex is thought to play a structural role in ensuring membrane stability and force transduction during muscle contraction. The multiple binding sites and domains present in the DAPC confer the scaffold of various signalling and channel proteins, which may implicate the DAPC in regulation of signalling processes. The DAPC is thought for instance to anchor a variety of signalling molecules near their sites of action. The dystroglycan complex may participate in the transduction of extracellular-mediated signals to the muscle cytoskeleton, and β-dystroglycan was shown to be involved in MAPK and Rac1 small GTPase signalling. More generally, dystroglycan is view as a cell surface receptor for extracellular matrix proteins. The adaptor proteins syntrophin contribute to recruit and regulate various signalling proteins such as ion channels, into a macromolecular complex. Although dystrophin and dystroglycan can be directly involved in signalling pathways, syntrophins play a central role in organizing signalplex anchored to the dystrophin scaffold. The dystrophin associated complex, can bind up to four syntrophin through binding domains of dystrophin and dystrobrevin, allowing the scaffold of multiple signalling proteins in close proximity. Multiple interactions mediated by PH and PDZ domains of syntrophin also contribute to build a complete signalplex which may include ion channels, such as voltage-gated sodium channels or TRPC cation channels, together with, trimeric G protein, G protein-coupled receptor, plasma membrane calcium pump, and NOS, to enable efficient and regulated signal transduction and ion transport. This article is part of a Special Issue entitled: Reciprocal influences between cell cytoskeleton and membrane channels, receptors and transporters. Guest Editor: Jean Claude Hervé.     

Fluorescent sensors reveal subcellular thermal changes

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Fluorescent europium-modified polymer nanoparticles for rapid and sensitive anthrax sensors

Novel fluorescent polyacrylonitrile nanoparticles were synthesized by microemulsion polymerization and Schiff base modification. By further modification with europium, the polyacrylonitrile nanoparticles could be used as a highly sensitive and rapid sensor for Bacillus anthracis spore detection in aqueous solution. The europium-modified polyacrylonitrile nanoparticles were readily combined with dipicolinic acid as a unique biomarker of B. anthracis, leading to high fluorescence emission. These nanoparticles enabled ratiometric detection without instrument-specific calibration due to the internal fluorescence reference. Additionally, the europium-modified polyacrylonitrile nanoparticle sensors exhibited a remarkable limit of detection (10pM) for dipicolinic acid and outstanding selectivity (160×) over aromatic ligands in aqueous solution. The ultrafine nanoparticle sensor showed a high capability for detecting anthrax due to the increased surface area-to-volume ratio and enhanced dispersibility.     

Secretory proteins as markers for cellular phenotypes in rat salivary glands

The neonatal submandibular glands (SMG) of the rat contain two types of cells: Type III cells secrete a group of proteins in response to beta-adrenergic stimulation, and Type I cells secrete a different protein, called Protein C (89 kDa), in response to cholinergic stimuli (Ball and Redman, 1984). Polyclonal antibodies raised to Protein B1 (26 kDa) showed that the several proteins in the B1-Immunoreactive Protein (B1-IP) group are localized exclusively to Type III cells. Although we expected that antibodies to Protein B1 would label only the submandibular gland, we found instead that the serous demilunes of the sublingual gland (SLG) and the acinar cells and intercalated ducts of the parotid gland (PRG) were strongly reactive in both the neonate and the adult. Immunoelectrophoretic analysis of gland extracts showed the major reactive species in the sublingual gland to have different mobilities than the B1-IP. On the other hand, reactive species in the parotid gland had mobilities identical to those of two SMG proteins. In the adult SMG, the neonatal Type I and Type III cells are not present, and the acinar cells are devoid of B1-IP reactivity; however, the cells of the intercalated ducts have components reactive with anti-B1 antibodies, and these do not appear to be identical to any neonatal bands. In contrast to the submandibular gland, the adult parotid and sublingual glands retain the localization of B1-IP reactivity in PRG acinar and intercalated duct cells and in SLG demilunes, and they show the neonatal immunoelectrophoretic pattern. This raises the possibility that the major B1-IP species in the adult PRG may be identical to transient proteins of the neonatal SMG.     

Type-3 copper proteins as biocompatible and reusable oxygen sensors

Fluorescently labeled type-3 copper proteins have been proposed previously as solution oxygen sensors by using a FRET mechanism. Herein, we describe how this principle can be adapted to sense O₂ by means of proteins immobilized in optically transparent silica matrices. Specifically, the protein, hemocyanin from Octopus vulgaris N-terminally labeled with Cy5, is immobilized in two different kinds of optically transparent silica matrices, which appear to be a promising platform for enzyme encapsulation. The presented results provide proof of principle that fluorescently labeled proteins immobilized in a silica matrix can be implemented in a reusable, biocompatible and stable oxygen measuring device that might lead to new developments in the field of optical biosensing.     

Genotypic temperature adaptations of cellular functions and proteins in two Zostera species

Summary The thermostability of protoplasmic streaming, the capacity for plasmolysis and reduction of tetrazolium salt, and the thermostability of acid phosphatase and peroxidase were compared in two species of Zostera, Z. marina L. and Z. noltii Hornem. which were growing in Sevastopal Bay on the Black Sea. The thermostability of studied functions and enzymes in Z. noltii is approximately 4° or 5° C higher than that in Z. marina and this is consistent with the greater thermophily of Z. noltii, which has a more southerly habitat and which is a less deep-water form than Z. marina. The adaptive significance of the correlation between function and protein thermostability and the environmental temperature is regarded as the adjustment of the level of protein flexibility to a prevailing ambient temperature.     

Evolutionarily conserved and nonconserved cellular localizations and functions of human SIRT proteins

Sir2 is a NAD+-dependent protein deacetylase that extends lifespan in yeast and worms. This study examines seven human proteins homologous to Sir2 (SIRT1 through SIRT7) for cellular localization, expression profiles, protein deacetylation activity, and effects on human cell lifespan. We found that: 1) three nuclear SIRT proteins (SIRT1, SIRT6, and SIRT7) show different subnuclear localizations: SIRT6 and SIRT7 are associated with heterochromatic regions and nucleoli, respectively, where yeast Sir2 functions; 2) SIRT3, SIRT4, and SIRT5 are localized in mitochondria, an organelle that links aging and energy metabolism; 3) cellular p53 is a major in vivo substrate of SIRT1 deacetylase, but not the other six SIRT proteins; 4) SIRT1, but not the other two nuclear SIRT proteins, shows an in vitro deacetylase activity on histone H4 and p53 peptides; and 5) overexpression of any one of the seven SIRT proteins does not extend cellular replicative lifespan in normal human fibroblasts or prostate epithelial cells. This study supports the notion that multiple human SIRT proteins have evolutionarily conserved and nonconserved functions at different cellular locations and reveals that the lifespan of normal human cells, in contrast to that of lower eukaryotes, cannot be manipulated by increased expression of a single SIRT protein.