Affinity labeling of the myosin ATPase with ribose-modified fluorescent nucleotides and vanadate

Ribose-modified fluorescent nucleotide analogs, 3'-O-anthraniloyl and 3'-O-(N-methylanthraniloyl) derivatives of AT(D)P, dAT(D)P, CT(D)P, UT(D)P, IT(D)P, and GT(D)P, were synthesized for use as substrates and affinity labels for the myosin ATPase [Hiratsuka, T. (1983) Biochim. Biophys. Acta 742, 496-508]. None of the fluorescent nucleoside triphosphate (NTP) analogs was significantly different from the corresponding natural NTP in its ability to support superprecipitation of actomyosin. When fluorescent and natural NTPs were used as substrates for the myosin subfragment-1(S-1) ATPase in the presence of 1mM vanadate ion (V1), a slight initial inhibition of the S-1 NTPase was followed by progressive inhibition to more than 60% over a period of 1 h. The apparent second-order rate constants were 0.14-0.44M-1 . s-1, suggesting the formation of the inactive fluorescent NDP-labeled S-1. After incubation of S-1 with the nucleoside diphosphate (NDP) analog in the presence of Vi, the resultant fluorescent NDP-labeled S-1 was isolated free of unbound Vi and the analog by gel filtration. The isolated complexes had stoichiometries of 0.6-1.1 NDP analog per S-1 active site. Native polyacrylamide gel electrophoresis revealed conveniently that the NDP analog is associated with S-1 as indicated by two intense fluorescent bands corresponding to S-1 isozymes. On dissociating gels, the analog was released from S-1, suggesting that the labeled S-1 is held together by strong secondary forces rather than covalent bonds.(ABSTRACT TRUNCATED AT 250 WORDS)     

Synthesis of a fluorescent 7-methylguanosine analog and a fluorescence spectroscopic study of its reaction with wheatgerm cap binding proteins.

In the initiation of protein synthesis, the mRNA 5'-terminal 7-methylguanosine cap structure and several recognition proteins play a pivotal role. For the study of this cap binding reaction, one approach is to use fluorescence spectroscopy. A ribose diol-modified fluorescent cap analog, anthraniloyl-m7GTP (Ant-m7GTP), was designed and synthesized for this purpose. This fluorescent cap analog was found to have a high quantum yield, resistance to photobleaching and avoided overlap of excitation and emission wavelengths with those of proteins. The binding of Ant-m7GTP with wheatgerm initiation factors elF-4F and elF-(iso)4F was determined. The fluorescent cap analog and m7GTP had similar interactions with both cap binding proteins. Fluorescence quenching experiments showed that the microenvironment of Ant-m7GTP when bound to protein was hydrophobic.     

Synthesis of a fluorescent 2′3′-dideoxycytosine analog,tCdd

The pathway leading to the preparation of a novel tricyclic 2′3′-dideoxycytosine analog, tCdd (1) is reported. A protected 2′3′-dideoxyribose prepared from l-glutamic acid was coupled to a silylated fluorescent base to yield a mixture of the α- and β-anomers of the 2′3′-dideoxyribonucleoside of 1,3-diaza-2-oxophenothiazine, tCdd (1). The fluorescent base analog retains a high fluorescence emission over a large pH range and should be useful in a variety of probe applications.     

Dominant affectors in the calmodulin network shape the time courses of target responses in the cell

In endothelial cells nitric oxide synthase is a dominant affector in the calmodulin network by virtue of its ability to bind a significant fraction of limiting intracellular calmodulin. We have investigated how this affector function influences the kinetics of calmodulin-dependent signaling in cells co-expressing the synthase and a fluorescent calmodulin target analog similar in its interactions with calmodulin to myosin light chain kinase. The synthase binds (Ca(2+))(4)-calmodulin with a K(d) value of approximately 0.2 nM and an association rate constant of approximately 1.5 x 10(5) M(-1) s(-1). These values are, respectively, 10- and 100-fold smaller than the corresponding values for the analog. Thus, when Ca(2+) is added to a mixture of calmodulin, target analog and synthase in vitro a large fluorescence transient with a relaxation time of approximately 600 s is observed as (Ca(2+))(4)-calmodulin is rapidly bound to the analog and then slowly captured by the higher affinity synthase. A rapid increase in the free Ca(2+) concentration elicits similar transient analog responses in cells expressing the cytoplasmic target analog and either a wild-type membrane bound or mutant cytoplasmic synthase. Transient responses are not observed in cells co-expressing the fluorescent analog and a mutant T497D synthase unable to bind calmodulin. These results demonstrate that dominant affectors in the calmodulin network shape both the magnitudes and time courses of target responses in the cell.     

The synthesis and properties of a functional fluorescent cholesterol analog

The synthesis of a new fluorescent cholesterol analog is described. The analog contains a cholesterol nucleus attached via a hydrophilic spacer to N-4-nitrobenzo-2-oxa-1,3-diazole. Since the cholesterol moiety is not perturbed this molecule probably interacts with lipid bilayers in much the same way as cholesterol itself does. The compound can be readily incorporated into small unilamellar vesicles by sonicating a mixture of it with egg yolk phosphatidylcholine in a buffer. Furthermore, the analog can be incorporated into preformed membranes either by exchange from vesicles containing the analog or by uptake from sonicated micelles of the analog. Thus this analog shows potential as a useful tool for studying the interactions of cholesterol with cell membranes.     

Synthesis and site-specific incorporation of a simple fluorescent pyrimidine

We describe procedures for the synthesis of a fluorescent pyrimidine analog and its site-specific incorporation into a DNA oligomer. The 5'-protected and 3'-activated nucleoside 4 is synthesized in three steps with an overall yield of 40%. Site-specific incorporation into a DNA oligomer occurs with greater than 88% coupling efficiency. This isosteric fluorescent DNA analog can be used to monitor denaturation of DNA duplexes via fluorescence and can positively detect the presence of abasic sites in DNA duplexes. The total time for synthesis of the phosphoramidite 4 is about 75 h, whereas the total time for site-specific incorporation of nucleoside 2 into an oligonucleotide and purification of the corresponding oligonucleotide is about 114 hours.     

Distinct structures of ATP and GTP complexes in the myosin ATPase

The active site of the myosin subfragment-1 ATPase was affinity-labeled with ribose-modified fluorescent analogs of ADP, dADP, CDP, UDP, IDP, and GDP in combination with vanadate, forming a stable myosin-nucleoside diphosphate-vanadate complex that is analogous to the normal myosin-ADP-Pi intermediate [Hiratsuka, T. (1984) J. Biochem. 96, 147-154]. Labeled enzyme was isolated free of unbound analog and vanadate, and fluorescent properties of the fluorophore at the active site were examined. Fluorescence emission and acrylamide quenching studies revealed that the hydrophobicity of environment around the fluorophore and the degree of its burial in the protein vary with the base structure of NDP. It was found that the fluorophore of ADP analog is most buried into the protein, while that of the GDP analog is least buried. The results suggest that the deep burial of ATP into the myosin active site is essential for muscle contraction.     

Phase transitions of alkyl ether analogs of phosphatidylcholine

The phase-transition temperatures of aqueous dispersions of diester, monoether and diether analogs of phosphatidylcholine were determinmed using transparinaric acid as a fluorescent probe. The diether analog of phosphatidylcholine has a higher phase-transition temperature, whilst the monoether analog has a lower phase-transition temperature than their diester counterpart.     

A pyrimidopyrimidoindole nucleoside (dC PPI): photophysical properties and thermal stability of the modified DNA duplexes

A new fluorescent deoxycytidine analog, 10-(2-deoxy-beta -D-ribofuranosyl)-pyrimido[4',5' :4,5]-pyrimido[1,6-a]indole-6,9(7H)-dione (dC(PPI)) was synthesized. Its fluorescent properties were studied in detail. It was found that this fluorescent nucleoside dC(PPI) could be used as a fluorescent label for DNA probes with minimal disturbance of their overall structure.     

Trace level detection of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) by microimmunosensor.

Reported in this paper is the development and characterization of a highly sensitive microcapillary immunosensor for the detection of the explosive, hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX). The immunosensor exploits antibodies as recognition elements for target antigens, fluorescence dye conjugates for reporter molecules and fused silica microcapillaries for its high surface-to-volume ratio. Detection of RDX with the microcapillary immunosensor requires covalent immobilization of anti-RDX antibodies on the inner core of the microcapillaries via heterobifunctional cross-linker chemistry. Subsequent saturation of all antibody binding domains follows with a synthetically prepared fluorescent analog of RDX. Displacement immunoassays were performed with the microcapillary immunosensor with the injection of unlabeled RDX at concentration levels from 1 part-per-trillion (pptr) to 1000 part-per-billion (ppb). As unlabeled RDX reaches the binding domain of the antibody, fluorescent RDX analog is displaced from the antibody, flows downstream and is measured by a spectrofluorometer. Fluorescence measurements of the displaced fluorescent RDX analog were equated to a standard calibration curve to quantify sample concentration. Complete evaluation of the RDX microcapillary immunosensor for selectivity and sensitivity was performed based on the following criteria: variable flow rates, antibody cross-reactivity, reproducibility and cross-linker (carbon spacer) comparison. Results indicate the lowest detectable limit (LDL) for RDX is 10 pptr (ng/l) with a linear dynamic range from 0.1 to 1000 ppb (ug/l).     

Synthesis and Hybridization Studies of Oligonucleotide Sequences with Modified Fluorescent Nucleoside Analogs

Abstract

Two complementary oligodeoxynucleotide hexamers CATGAA and TTCATG and a pentamer with a fluorescent nucleoside analog viz. 9-N-(2′-deoxy-β-D-ribofuranosyl) carbazole (C*) incorporated into it, TTC*ATG were synthesized and characterised by spectroscopic and chromatographic studies. The comparative fluorescent studies of the two nucleoside analogs viz. 9-N-(2′-deoxy-β-D-ribofuranosyl) acridone and its carbazole analog (C*) have been carried out under different experimental conditions. The effect on fluorescence by incorporation of (C*) into the sequence and its subsequent hybridization with the complementary sequence have been studied.     

A new,long-wavelength borondipyrromethene sphingosine for studying sphingolipid dynamics in live cells

Sphingolipids function as cell membrane components and as signaling molecules that regulate critical cellular processes. To study unacylated and acylated sphingolipids in cells with fluorescence microscopy, the fluorophore in the analog must be located within the sphingoid backbone and not the N-acyl fatty acid side chain. Although such fluorescent sphingosine analogs have been reported, they either require UV excitation or their emission overlaps with that of the most common protein label, green fluorescent protein (GFP). We report the synthesis and use of a new fluorescent sphingolipid analog, borondipyrromethene (BODIPY) 540 sphingosine, which has an excitation maximum at 540 nm and emission that permits its visualization in parallel with GFP. Mammalian cells readily metabolized BODIPY 540 sphingosine to more complex fluorescent sphingolipids, and subsequently degraded these fluorescent sphingolipids via the native sphingolipid catabolism pathway. Visualization of BODIPY 540 fluorescence in parallel with GFP-labeled organelle-specific proteins showed the BODIPY 540 sphingosine metabolites were transported through the secretory pathway and were transiently located within lysosomes, mitochondria, and the nucleus. The reported method for using BODIPY 540 sphingosine to visualize sphingolipids in parallel with GFP-labeled proteins within living cells may permit new insight into sphingolipid transport, metabolism, and signaling.     

Formation of beta,gamma-methylene-7,8-dihydroneopterin 3'-triphosphate from beta,gamma-methyleneguanosine 5'-triphosphate by GTP cyclohydrolase I of Escherichia coli

GTP cyclohydrolase I of Escherichia coli converts [beta,gamma-methylene] GTP to a fluorescent product that is characterized as [beta,gamma-methylene]dihydroneopterin triphosphate. Interaction between the GTP analog and the enzyme gave a Ki of 3.0 microM, which may be compared to the Km of 0.1 microM for GTP. This new analog of dihydroneopterin triphosphate may, in turn, be converted to the same greenish-yellow pteridines (compounds X, X1, and X2) that are obtained from dihydroneopterin triphosphate. Because of its stability to phosphatase action, this analog may be useful for studies in pteridine metabolism.     

Transfer of cholesterol and a fluorescent cholesterol analog, 3'-pyrenylmethyl-23,24-dinor-5-cholen-22-oate-3 beta-ol, between human plasma high density lipoproteins

A fluorescent cholesterol analog, 3'-pyrenylmethyl-23,24-dinor-5-cholen-22-oate-3 beta-ol (PMCA), has been synthesized as a spectroscopic probe of cholesterol function. The substrate activity of PMCA, about two-thirds that of cholesterol, with lecithin:cholesterol acyltransferase indicates that PMCA is a reasonable cholesterol analog and that the orientation of the substituted sterol in the phospholipid interface is similar to that of cholesterol. The fluorescence properties of PMCA are similar to those of other pyrene-containing compounds that exhibit concentration-dependent excimer fluorescence. The rate of transfer of [3H]PMCA between HDL is about six times faster than cholesterol. These results indicate that the analog will be useful in studies of cholesterol function.     

Receptor-mediated endocytosis of tuftsin by macrophage cells

A fluorescent analog of the phagocytosis stimulating peptide tuftsin was prepared by coupling tetramethyl rhodamine isothiocyanate to a C-terminal elongated derivative of tuftsin. This analog, Thr-Lys-Pro-Arg-Gly-Lys(N epsilon-tetramethyl rhodamine)-OH, was used to visualize tuftsin receptors on mice macrophage cells by fluorescent image intensification. Fluorescent labelling was carried out at 37 degrees C, using a concentration of 200 nM and 2 microM of the fluorescent tuftsin derivative. The formation of peptide-receptor clusters and their subsequent internalization, as discerned by image intensification, were rapid processes, 5 min and 5-30 min, respectively. Preincubation of macrophages with tuftsin for various time intervals, followed by quantification of the tuftsin receptor using radiolabelled tuftsin, suggest that tuftsin receptors are initially increased in amount (5-7 min) and subsequently reduced (after 10-15 min) as judged by sites available for tritiated tuftsin. The binding studies are rather complementary to the fluorescence observations and support the assumption that the tuftsin receptor on the membrane of the mice macrophage cell is rapidly mobilized.     

Evaluation of fluorescently labeled xylopyranosides as probes for proteoglycan biosynthesis

A new fluorescent analog to the antiproliferative 2-(6-hydroxynaphthyl)-beta-d-xylopyranoside has been synthesized and tested on a T24 cell line. The new analog was efficiently uptaken by the T24 cells but did not initiate priming of GAG chains. The results are similar to other fluorescently labeled analogs and we propose that these compounds are too large and unpolar to efficiently function as GAG-primers.     

Empirical model and in vivo characterization of the bacterial response to synthetic gene expression show that ribosome allocation limits growth rate

Synthetic biology uses modeling to facilitate the design of new genetic constructions. In particular, it is of utmost importance to model the reaction of the cellular chassis when expressing heterologous systems. We constructed a mathematical model for the response of a bacterial cell chassis under heterologous expression. For this, we relied on previous characterization of the growth-rate dependence on cellular resource availability (in this case, DNA and RNA polymerases and ribosomes). Accordingly, we estimated the maximum capacities of the cell for heterologous expression to be 46% of the total RNA and the 33% of the total protein. To experimentally validate our model, we engineered two genetic constructions that involved the constitutive expression of a fluorescent reporter in a vector with a tunable origin of replication. We performed fluorescent measurements using population and single-cell fluorescent measurements. Our model predicted cell growth for several heterologous constructions under five different culture conditions and various plasmid copy numbers with significant accuracy, and confirmed that ribosomes act as the limiting resource. Our study also confirmed that the bacterial response to synthetic gene expression could be understood in terms of the requirement for cellular resources and could be predicted from relevant cellular parameters.     

Preparation of Actin and Fluorescent Actin Analogs from Plant Cells

The plant actin cytoskeleton provides a dynamic cytoplasmic framework for many fundamental cellular processes like cytoplasmic streaming,cytokinesis and morphogenesis.Understanding the actin organization and structure in plants requires the generation of new probes for measuring actin dynamics in living cells. Fluorescent analog cytochemistry presents an unrivaled opportunity to probe the actin cytoskeleton in living cells. Such method using in the study of plant actin cytoskeleton has not been reported. By using this method, based on the affinity chromatography of profilin with PLP-Sepharose (PLP: poly-L-proline) for actin purification, the author obtained 6 mg of > 98% in purity, polymerizable actin from 10 g of maize (Zea mays L. ) pollen, and this actin was successfully labeled with Oregon Green 488 carboxylic acid. From 10 g of maize pollen, 1.2 mg with 60 % dye/protein ratio, polymerizable, fluorescent actin analog was obtained. The study yields an effective method for purifying plant actin and preparing fluorescent analog, which may provide facilities for the study of actin dynamics in plant ceils.     

植物肌动蛋白的纯化及荧光标记

以植物花粉为材料,利用肌动蛋白可以与其单体结合蛋白———profilin特异性结合的特性及profilin的多聚脯氨酸亲和柱层析法,获得较大量、高纯度,具有活性的植物肌动蛋白,并用羧酸俄勒冈绿对所获纯化肌动蛋白进行了荧光标记。结果显示,从10g玉米(ZeamaysL.)花粉中可得到1.2mg具有绿色荧光的肌动蛋白,标记率为60%。体外实验结果表明,所得荧光肌动蛋白在适宜条件下可聚合成绿色荧光微丝。     

Localization of fluorescent substances in the cellular slime moldDictyostelium discoideum cells during growth and development

The localization of fluorescent substance was observed microscopically in livingDictyostelium discoideum cells. The fluorescence was localized in the vacuoles of the vegetative cells. The fluorescent vacuoles were not observed in the dead cells. The fluorescent vacuoles in the cytoplasm were lost in starved cells which are able to form an aggregate and to differentiate. The fluorescent vacuoles were not lost but decreased slightly in the cytoplasm of full grown cells and of cells grown in liquid nutrient medium for an extended period of time (stationary phase cells). On a solid substratum, fluorescent vacuoles were also lost from the cells, where the vegetative cells aggregate and form a slug-shaped mass of cells. The whole slug showed homogeneous fluorescence. In a finally constructed fruiting body, the spore mass showed fluorescence. In a spore mass, the fluorescence was not observed in the spores but in the interspore space of the spore mass. It is suggested that vegetative cells secrete fluorescent substance into the inter-cellular space in the mass of cells during development.