Effect of phospholipid:protein ratio on the state of aggregation of the (Ca2+-Mg2+)-ATPase

The organization of the (Ca2+-Mg2+)-ATPase has been studied in reconstituted systems by fluorescence polarization of the ATPase labeled with fluorescein isothiocyanate (FITC) and resonance energy transfer between ATPase labeled with FITC and with eosin isothiocyanate (EITC). The fluorescence polarization of FITC-ATPase was found to decrease with increasing labeling ratio FITC:ATPase, indicating depolarization as a result of resonance energy transfer between ATPase molecules. Fluorescence polarization was, however, independent of the molar ratio of phospholipid to protein above a molar ratio of 50:1. Resonance energy transfer between FITC-ATPase and EITC-ATPase was also found to be independent of phospholipid:protein ratio. It is suggested therefore that the ATPase is not randomly distributed in the plane of the membrane but rather forms ordered clusters (probably rows of monomers or dimers) on the fluorescence time scale (nanoseconds) even in the presence of a large excess of phospholipid. This organization within the membrane is dependent both on the chemical structure of the phospholipid and on its physical phase.     

1H and 15N NMR resonance assignments and secondary structure of titin type I domains

Titin/connectin is a giant muscle protein with a highly modular architecture consisting ofmultiple repeats of two sequence motifs, named type I and type II. Type I modules have beensuggested to be intracellular members of the fibronectin type III (Fn3) domain family. Alongthe titin sequence they are exclusively present in the region of the molecule located in thesarcomere A-band. This region has been shown to interact with myosin and C-protein. Oneof the most noticeable features of type I modules is that they are particularly rich insemiconserved prolines, since these residues account for about 8% of their sequence. We havedetermined the secondary structure of a representative type I domain (A71) by 15N and 1HNMR. We show that the type I domains of titin have the Fn3 fold as proposed, consisting ofa three- and a four-stranded -sheet. When the two sheets are placed on top of each other toform the -sandwich characteristic of the Fn3 fold, 8 out of 10 prolines are found on the sameside of the molecule and form an exposed hydrophobic patch. This suggests that thesemiconserved prolines might be relevant for the function of type I modules, providing asurface for binding to other A-band proteins. The secondary structure of A71 was structurallyaligned to other extracellular Fn3 modules of known 3D structure. The alignment shows thattitin type I modules have closest similarity to the first Fn3 domain of Drosophila neuroglian.     

Origin of a fluorescence increase accompanying the limited proteolysis of fluorescein-labeled human prothrombin by Factor Xa

In a search for a probe which would report its proteolysis to thrombin, the human blood coagulation zymogen prothrombin was covalently labeled with fluorescein. Fluorescein isothiocyanate (FITC) and dichlorotriazinylaminofluorescein (DCTAF) both introduced approximately 1 molecule of dye, but labeling occurred at different locations, as FITC had no effect on clotting activity whereas DCTAF caused 95% inactivation. At pH 9.0 DCTAF, but not FITC, could induce labeling up to 4 mol/mol. All derivatives were activated normally by prothrombinase (the activating complex of Factor Xa, Factor V(a), Ca2+ and phospholipids), as indicated by the pattern of bands on SDS gel electrophoresis and an unaltered yield of activity toward a chromogenic substrate for thrombin. Upon undergoing this limited proteolysis, the most heavily labeled derivative showed a 40% increase in fluorescence of the fluorescein at 520 nm (lambda ex 480 nm). In contrast, the fluorescence of lightly labeled forms was more intense but increased by only 0-5% upon activation. The data suggest that the lower fluorescence of the most labeled form is due to an intramolecular quenching effect between the dye molecules on individual polypeptide chains that is partly relieved when activation occurs.     

近场扫描光学成像结合量子点标记的纳米技术在细胞生物学中的应用

近场扫描光学显微镜（NSOM）对传统的光学分辨极限产生了革命性的突破,可在超高光学分辨率下无侵人性和无破坏性地对生物样品进行观测。量子点（QDs）具有极好的光学性能,如荧光寿命长、激发谱宽、生物相容性强、光稳定性好等优点,适合先进的生物成像。NSOM结合QDs标记的纳米技术被应用在细胞生物学中。通过纳米量级NSOM免疫荧光成像（50nm）对特定蛋白分子在细胞表面的动态分布进行可视化研究和数量化分析,阐明了蛋白分子在不同细胞过程中的作用机制。因此,NSOM／QD基成像系统提供了单个蛋白分子最高分辨率的荧光图像,为可视化研究蛋白分子机制的提供了一种强有力的工具。     

Ail protein binds ninth type III fibronectin repeat (9FNIII) within central 120-kDa region of fibronectin to facilitate cell binding by Yersinia pestis

The Yersinia pestis adhesin molecule Ail interacts with the extracellular matrix protein fibronectin (Fn) on host cells to facilitate efficient delivery of cytotoxic Yop proteins, a process essential for plague virulence. A number of bacterial pathogens are known to bind to the N-terminal region of Fn, comprising type I Fn (FNI) repeats. Using proteolytically generated Fn fragments and purified recombinant Fn fragments, we demonstrated that Ail binds the centrally located 120-kDa fragment containing type III Fn (FNIII) repeats. A panel of monoclonal antibodies (mAbs) that recognize specific epitopes within the 120-kDa fragment demonstrated that mAb binding to (9)FNIII blocks Ail-mediated bacterial binding to Fn. Epitopes of three mAbs that blocked Ail binding to Fn were mapped to a similar face of (9)FNIII. Antibodies directed against (9)FNIII also inhibited Ail-dependent cell binding activity, thus demonstrating the biological relevance of this Ail binding region on Fn. Bacteria expressing Ail on their surface could also bind a minimal fragment of Fn containing repeats (9-10)FNIII, and this binding was blocked by a mAb specific for (9)FNIII. These data demonstrate that Ail binds to (9)FNIII of Fn and presents Fn to host cells to facilitate cell binding and delivery of Yops (cytotoxins of Y. pestis), a novel interaction, distinct from other bacterial Fn-binding proteins.     

Spatial organization of CaATPase molecules in sarcoplasmic reticulum vesicles

Fluorescence intensity, polarization, and (Ca2+-Mg2+)-ATPase (CaATPase) activity were measured for sarcoplasmic reticulum (SR) CaATPase with varying amounts of fluorescein isothiocyanate (FITC) attached at a specific site at or near the ATP binding site. The stoichiometry of attached FITC was proportional to the inhibition of ATPase activity, consistent with the independent labeling of one FITC site per CaATPase molecule. Polarization measurements on vesicular CaATPase indicated the occurrence of energy-transfer depolarization that increased as the fraction of binding sites labeled by FITC increased. Addition of the nonionic detergent dodecyl nonaoxyethylene alcohol (C12E9) eliminated the energy-transfer depolarization for all degrees of labeling with little direct effect on the attached FITC molecule. Fluorescence polarization measurements on sizing-column-purified FITC-labeled CaATPase in the presence of 30 mM C12E9 indicated that the sample consisted of homogeneous monomeric CaATPase. The attached FITC molecule was not sensitive to the bulk viscosity for either the vesicular or the detergent-solubilized CaATPase. The midpoints of the transition from vesicular to monomeric CaATPase as a function of increasing detergent concentration were determined from fluorescence polarization and light-scattering measurements. The dependence of these midpoints on the CaATPase concentration indicated a stoichiometry of 262 +/- 35 molecules of C12E9 per CaATPase in the detergent-protein complex. Both measurements gave the same result. The decrease of fluorescence polarization with increasing saturation of the FITC binding sites for vesicular and detergent-solubilized CaATPase was analyzed in terms of energy-transfer depolarization to determine the spatial arrangements of CaATPase molecules.(ABSTRACT TRUNCATED AT 250 WORDS)     

N－糖链在纤连蛋白分泌及纤连蛋白受体与配体结合中的作用

应用能阻断糖蛋白Ｎ－糖链合成的衣霉素（ＴＭ）,研究了Ｎ－糖链缺失对ＨＴ１０８０细胞分泌纤连蛋白（Ｆｎ）以及纤连蛋白受体（ＦｎＲ）与配体结合的影响。结果发现,１μｇ／ｍｌ的ＴＭ可抑制Ｎ－糖链的合成（此时,３Ｈ－甘露糖掺入下降６３％）,但细胞分泌Ｆｎ的量仅下降３３％,这主要是由于蛋白合成受ＴＭ抑制（２５％）而引起,因而,Ｎ－糖链缺失可能并不影响Ｆｎ的分泌。而在同样条件下,单个细胞结合１２５Ｉ－Ｆｎ的量显著下降,显示Ｎ－糖链的缺失可能导致了膜上ＦｎＲ总量或其与配体结合的亲和力的改变。ＴＭ处理组的ＦｎＲ的内吞率与对照组相比较无明显差异,提示受体分子中的Ｎ－糖链缺失不影响其内吞过程．     

Imaging proteins inside cells with fluorescent tags

Watching biological molecules provides clues to their function and regulation. Some of the most powerful methods of labeling proteins for imaging use genetically encoded fluorescent fusion tags. There are four standard genetic methods of covalently tagging a protein with a fluorescent probe for cellular imaging. These use (i) autofluorescent proteins, (ii) self-labeling enzymes, (iii) enzymes that catalyze the attachment of a probe to a target sequence, and (iv) biarsenical dyes that target tetracysteine motifs. Each of these techniques has advantages and disadvantages. In this review, we cover new developments in these methods and discuss practical considerations for their use in imaging proteins inside living cells.     

Assay to mechanically tune and optically probe fibrillar fibronectin conformations from fully relaxed to breakage

In response to growing needs for quantitative biochemical and cellular assays that address whether the extracellular matrix (ECM) acts as a mechanochemical signal converter to co-regulate cellular mechanotransduction processes, a new assay is presented where plasma fibronectin fibers are manually deposited onto elastic sheets, while force-induced changes in protein conformation are monitored by fluorescence resonance energy transfer (FRET). Fully relaxed assay fibers can be stretched at least 5-6 fold, which involves Fn domain unfolding, before the fibers break. In native fibroblast ECM, this full range of stretch-regulated conformations coexists in every field of view confirming that the assay fibers are physiologically relevant model systems. Since alterations of protein function will directly correlate with their extension in response to force, the FRET vs. strain curves presented herein enable the mapping of fibronectin strain distributions in 2D and 3D cell cultures with high spatial resolution. Finally, cryptic sites for fibronectin's N-terminal 70-kD fragment were found to be exposed at relatively low strain, demonstrating the assay's potential to analyze stretch-regulated protein-protein interactions.     

糖链结构不同的纤连蛋白与HT1080细胞结合研究

人血浆纤连蛋白（Ｆｉｂｒｏｎｅｃｔｉｎ,Ｆｎ）与人胎盘纤连蛋白两者在肽链结构上基本相同,但人血浆Ｆｎ的Ｎ－糖链结构为二天线结构,而人胎盘Ｆｎ不仅Ｎ－糖链的数量增加,同时还含有多天线结构,分别用~（１２５）Ｉ标记这两种具有不同糖链结构的Ｆｎ,观察两者与ＨＴ１０８０细胞的饱和结合的亲和性,结果发现,在４℃,人血浆Ｆｎ与ＨＴ１０８０细胞的饱和结合为１２９ｎｇ／１０~５细胞,解离常数为２．８３×１０~（－８）ｍｏｌ／Ｌ,人胎盘Ｆｎ与ＨＴ１０８０细胞的饱和结合为１３３ｎｇ／１０~６细胞,解离常数为２．６４×１０~（－８）ｍｏｌ／Ｌ．因而,人血浆Ｆｎ与人胎盘Ｆｎ上Ｎ－糖链的不同并未影响其与受体的结合．     

Fluorescence Tracing of Intracellular Proteins

Developments in fluorescence microscopy and the availability of fluorescently labeled antibodies and probes for localization of molecules and organelles have made the microscope an indispensable tool with which one can map specific molecules to subcellular loci allowing deep insight into cell and organelle biology. Furthermore, confocal microscopy permits analysis of the three dimensional architecture of cells that could not be accomplished by conventional light microscopy. The goal of fluorescence protein tracing by microscopy is to visualize cellular constituents and general cytoarchitecture as close to native organization as possible. To achieve this, and to preserve cellular structure in the best possible manner, the specimen is usually fixed chemically. Here I review several standard fixation, permeabilization and labeling schemes followed by examples of several standard imaging techniques.     

Fluorescence ratio measurements of double-labeled probes for multiple in situ hybridization by digital imaging microscopy.

To expand the multiplicity of the in situ hybridization (ISH) procedure, which is presently limited by the number of fluorochromes spectrally separable in the microscope, a digital fluorescence ratio method is proposed. For this purpose, chromosome-specific repetitive probes were double-labeled with two haptens and hybridized to interphase nuclei of human peripheral blood lymphocytes. The haptens were immunocytochemically detected with specific antibodies conjugated with the fluorochromes FITC or TRITC. The FITC and TRITC fluorescence intensities of spots obtained with different double-haptenized probes were measured, and the fluorescence ratio was calculated for each ISH spot. Combinations of different haptens, such as biotin, digoxigenin, fluorescein, sulfonate, acetyl amino fluorene (AAF), and mercury (Hg) were used. The fluorescence intensity ratio (FITC/TRITC) of the ISH spots was fairly constant for all combinations used, with coefficients of variation between 10 and 30%. To study the feasibility of a probe identification procedure on the basis of probe hapten ratios, one probe was double-labeled with different ratios, by varying the relative concentrations of the modified nucleotides (biotin-11-dUTP and digoxigenin-11-dUTP) in the nick-translation reaction. Measurement of the FITC and TRITC intensities of the ISH spots showed that the concentration of modified nucleotides used in the labeling procedures was reflected in the mean fluorescence intensity of the ISH spots. Furthermore, the ratio distributions showed little overlap due to the relatively small coefficients of variation. The results indicate that a multiple ISH procedure based on fluorescence ratio imaging of double-labeled probes is feasible.     

An Arsenic Fluorescent Compound as a Novel Probe to Study Arsenic-Binding Proteins

Arsenic-binding proteins are under continuous research. Their identification and the elucidation of arsenic/protein interaction mechanisms are important because the biological effects of these complexes may be related not only to arsenic but also to the arsenic/protein structure. Although many proteins bearing a CXXC motif have been found to bind arsenic in vivo, new tools are necessary to identify new arsenic targets and allow research on protein/arsenic complexes. In this work, we analyzed the performance of the fluorescent compound APAO-FITC (synthesized from p-aminophenylarsenoxide, APAO, and fluorescein isothiocyanate, FITC) in arsenic/protein binding assays using thioredoxin 1 (Trx) as an arsenic-binding protein model. The Trx-APAO-FITC complex was studied through different spectroscopic techniques involving UV?CVis, fluorescence, atomic absorption, infrared and circular dichroism. Our results show that APAO-FITC binds efficiently and specifically to the Trx binding site, labeling the protein fluorescently, without altering its structure and activity. In summary, we were able to study a protein/arsenic complex model, using APAO-FITC as a labeling probe. The use of APAO-FITC in the identification of different protein and cell targets, as well as in in vivo biodistribution studies, conformational studies of arsenic-binding proteins, and studies for the design of drug delivery systems for arsenic anti-cancer therapies, is highly promising.     

Protein synthesis as a function of protein content in exponentially growing NHIK 3025 cells studied by flow cytometry and cell sorting

Methods of cell preparation and quantitative flow cytometric cell sorting were developed for precise measurements of the incorporated radioactivity in cells labelled with [¹⁴C]-valine and fractionated as a function of their fluorescence intensity after staining with fluorescein-iso-thiocyanate (FITC). FITC fluorescence intensity of exponentially growing NHIK 3025 cells was found to be directly proportional to cellular protein content as measured by saturation-labelling with [¹⁴C]-valine. Protein synthesis as measured by ¹⁴C incorporation after pulse-labelling was found to increase nearly proportionally with cellular protein content. The deviations from proportionality were not greater than 6%, but yet found to be significant since the measurement error corresponded to only 2% standard deviation.     

Synthesis of 3′-O-Alkyl Homologues and a Biotin Probe of Isorhamnetin and Evaluation of Cytotoxic Efficacy on Cancer Cells

Isorhamnetin is a natural flavonoid which shows a variety of biological activities such as antioxidant, anti-inflammatory and antitumor. In order to identify the cellular binding protein of isorhamnetin as potential anti-cancer target, we first synthesized 3′-O-substituted quercetin as isorhamnetin homologues and evaluated the growth inhibitory activity of these derivatives on breast, colon and prostate cancer cell lines. The preliminary results showed that the 3′-O modification did not affect the cytotoxic activity of the scaffold. Analysis of the co-crystal structure and the docking pose of isorhamnetin with reported binding protein of isorhamnetin or quercetin indicated the 3′-O-substitution groups located outside of the binding pocket, which is in accordance with activity of 3′-O derivatives. Then a biotin conjugate of isorhamnetin with a tetraethylene glycol (PEG)₄ linker at the 3′ position was synthesized and the resulting probe retained the anti-proliferative activity on cancer cell lines, while the cellular fluorescence analysis showed the distribution of probe inside the cells which indicated the probe had limited cell permeability. Finally, pull down assay both in situ inside cells and in the cell lysates indicated the isorhamnetin biotin probe was capable of protein labeling in cell lysates. These findings provide the isorhamnetin 3′-O-biotin probe as a tool to reveal the target proteins of isorhamnetin.     

Utilization of fluorescent probes for the quantification and identification of subcellular proteomes and biological processes regulated by lipid peroxidation products

Oxidative modifications to cellular proteins are critical in mediating redox-sensitive processes such as autophagy, the antioxidant response, and apoptosis. The proteins that become modified by reactive species are often compartmentalized to specific organelles or regions of the cell. Here, we detail protocols for identifying the subcellular protein targets of lipid oxidation and for linking protein modifications with biological responses such as autophagy. Fluorophores such as BODIPY-labeled arachidonic acid or BODIPY-conjugated electrophiles can be paired with organelle-specific probes to identify specific biological processes and signaling pathways activated in response to oxidative stress. In particular, we demonstrate “negative” and “positive” labeling methods using BODIPY-tagged reagents for examining oxidative modifications to protein nucleophiles. The protocol describes the use of these probes in slot immunoblotting, quantitative Western blotting, in-gel fluorescence, and confocal microscopy techniques. In particular, the use of the BODIPY fluorophore with organelle- or biological process-specific dyes and chromophores is highlighted. These methods can be used in multiple cell types as well as isolated organelles to interrogate the role of oxidative modifications in regulating biological responses to oxidative stress.     

Force-induced unfolding of fibronectin in the extracellular matrix of living cells

Whether mechanically unfolded fibronectin (Fn) is present within native extracellular matrix fibrils is controversial. Fn extensibility under the influence of cell traction forces has been proposed to originate either from the force-induced lengthening of an initially compact, folded quaternary structure as is found in solution (quaternary structure model, where the dimeric arms of Fn cross each other), or from the force-induced unfolding of type III modules (unfolding model). Clarification of this issue is central to our understanding of the structural arrangement of Fn within fibrils, the mechanism of fibrillogenesis, and whether cryptic sites, which are exposed by partial protein unfolding, can be exposed by cell-derived force. In order to differentiate between these two models, two fluorescence resonance energy transfer schemes to label plasma Fn were applied, with sensitivity to either compact-to-extended conformation (arm separation) without loss of secondary structure or compact-to-unfolded conformation. Fluorescence resonance energy transfer studies revealed that a significant fraction of fibrillar Fn within a three-dimensional human fibroblast matrix is partially unfolded. Complete relaxation of Fn fibrils led to a refolding of Fn. The compactly folded quaternary structure with crossed Fn arms, however, was never detected within extracellular matrix fibrils. We conclude that the resting state of Fn fibrils does not contain Fn molecules with crossed-over arms, and that the several-fold extensibility of Fn fibrils involves the unfolding of type III modules. This could imply that Fn might play a significant role in mechanotransduction processes.     

Multicolor protein labeling in living cells using mutant β-lactamase-tag technology

Protein labeling techniques using small molecule probes have become important as practical alternatives to the use of fluorescent proteins (FPs) in live cell imaging. These labeling techniques can be applied to more sophisticated fluorescence imaging studies such as pulse-chase imaging. Previously, we reported a novel protein labeling system based on the combination of a mutant β-lactamase (BL-tag) with coumarin-derivatized probes and its application to specific protein labeling on cell membranes. In this paper, we demonstrated the broad applicability of our BL-tag technology to live cell imaging by the development of a series of fluorescence labeling probes for this technology, and the examination of the functions of target proteins. These new probes have a fluorescein or rhodamine chromophore, each of which provides enhanced photophysical properties relative to coumarins for the purpose of cellular imaging. These probes were used to specifically label the BL-tag protein and could be used with other small molecule fluorescent probes. Simultaneous labeling using our new probes with another protein labeling technology was found to be effective. In addition, it was also confirmed that this technology has a low interference with respect to the functions of target proteins in comparison to GFP. Highly specific and fast covalent labeling properties of this labeling technology is expected to provide robust tools for investigating protein functions in living cells, and future applications can be improved by combining the BL-tag technology with conventional imaging techniques. The combination of probe synthesis and molecular biology techniques provides the advantages of both techniques and can enable the design of experiments that cannot currently be performed using existing tools.     

A general strategy for site-specific double labeling of globular proteins for kinetic FRET studies

Site-directed mutagenesis provides a straightforward means of creating specific targets for chemical modifications of proteins. This capability enhanced the applications of spectroscopic methods adapted for addressing specific structural questions such as the characterization of partially folded and transient intermediate structures of globular proteins. Some applications such as the steady state or time-resolved fluorescence resonance energy transfer (FRET) detection of the kinetics of protein folding require relatively large quantities (approximately 10-100 mg) of site-specific doubly labeled protein samples. Engineered cysteine residues are common targets for labeling of proteins. The challenge here is to develop methods for selective modification of one of two reactive sulfhydryl groups in a protein molecule. A general systematic procedure for selective labeling of each of two cysteine residues in a protein molecule was developed, using Escherichia coli adenylate kinase (AKe) as a model protein. Potential sites for insertion of cysteine residues were selected by examination of the crystal structure of the protein. A series of single-cysteine mutants was prepared, and the rates of the reaction of each engineered cysteine residue with a reference reagent [5,5'-dithiobis(2-nitrobenzoic acid) (DTNB)] were determined. Two-cysteine mutants were prepared by selection of pairs of sites for which the ratio of this reaction rate constant was high (>80). The conditions for the selective labeling reaction were optimized. In a first cycle of labeling, the more reactive cysteine residue was labeled with a fluorescent probe (donor). The second probe was attached to the less reactive site under unfolding conditions in the second cycle of labeling. The doubly and singly labeled mutants retained full enzymatic activity and the capacity for a reversible folding-unfolding transition. High yields (70-90%) of the preparation of the pure, site-specific doubly labeled AK mutant were obtained. The procedure described herein is a general outline of procedures, which can meet the double challenge of both site specificity and large-scale preparation of doubly labeled proteins.