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A key feature of Parkinson's disease is the formation and accumulation of amyloid fibrils of the natively unfolded protein α-synuclein (ASN) inside neurons. Recently we have proposed novel sensitive monomethinecyanine dye T-284 as fluorescent probe for quantitative detection of ASN amyloid fibrils. In this study the T-284 dye complex with ASN fibril was characterized by means of fluorescence anisotropy, atomic force microscopy and time-resolved fluorescence techniques to give further insights into the mode of dye interaction with amyloid fibrils. The fluorescence anisotropy of T-284 was shown to noticeably increase upon addition of aggregated proteins indicating on stable dye/amyloid fibril complex formation. AFM imaging of fibrillar wild-type ASN revealed differences in heights between ASN fibrils alone and in presence of the T-284 dye (6.37 ± 1.0 nm and 8.0 ± 1.1 nm respectively), that is believed to be caused by embedding of T-284 dye molecules in the "binding channel" running along the fibril. Fluorescence decay analysis of the T-284 in complexes with fibrillar ASN variants revealed the fluorescence lifetime values for T-284/fibril complexes to be an order of magnitude higher as compared to the free dye. Also, the fluorescence decay of free T-284 was bi-exponential, while dye bound to protein yields tri-exponential decay. We suppose that in complexes with fibrillar ASN variants T-284 dye might exist in different "populations" due to interaction with fibrils in different conformers and ways. The exact binding mode of T-284 with ASN fibrils needs further studies. Studied parameters of dye/amyloid fibril complexes are important for the characterization and screening of newly-developed amyloid-sensitive dyes.

We examined the practical aspects of using fluorescent mono (T-284) and trimethinecyanine (SH-516) dyes for detecting and quantifying fibrillar alpha-synuclein (ASN). We studied the interaction of cyanine dyes with fibrillar proteins using fluorescence spectroscopy and atomic force microscopy. The commercially available classic amyloid stain thioflavin T (Thio T) was used as the reference dye. T-284 and SH-516 dyes can be used for fluorometric quantification of fibrillar wild-type ASN at concentrations of approximately 1.5-20 microg/ml. Both dyes appeared suitable for step-wise monitoring of ASN variants (wild-type and mutants A30P and A53T) aggregation into fibrils in vitro, demonstrating good reproducibility, exceeding that for the commonly used Thio T. Our assay may be used for screening in vitro of agents capable of affecting the aggregation of ASN. In addition, T-284 and SH-516 cyanine dyes were shown to recognize amyloid proteins of various amino acid compositions selectively. T-284 demonstrated particular sensitivity to wild-type and A53T ASN, while for SH 516, the fluorescence response to fibrillar proteins was nearly the same except for lysozymes. T-284 and SH-516 cyanine dyes are sensitive and specific fluorescent probes for monitoring ASN fibril formation process in vitro, quantification of fibrillar ASN in solution, and fluorescent detection of various fibrillar protein species.

The cytotoxic interaction between cloned human Natural Killer (NK) cells and K562 target cells was studied using confocal laser scanning microscopy (CLSM) and conventional fluorescence microscopy. We observed, using fixed as well as living cells, the occurrence of (pseudo)emperipolesis during the interaction. About 30% of conjugated NK cells penetrated, partly or completely, into the target cells (in-conjugation). Virtually all in-conjugated target cells exhibited polymerized actin. Killer cells of in-conjugates were frequently seen approaching the target cell nucleus or aligning along it. If the cytotoxic process was inhibited by the absence of calcium neither actin polymerization nor in-conjugation were observed. A kinetic study showed that in-conjugation starts somewhat later than actin polymerization but still within a few minutes after addition of calcium to conjugates previously formed in the absence of calcium. The presence of cytochalasin D (an inhibitor of actin polymerization) completely inhibited in-conjugation and partly reduced the cytotoxic activity. Zinc ions (endonuclease inhibition) inhibited in-conjugation and decreased the total number of target cells with polymerized actin in a concentration dependent manner. Cytotoxic activity was also reduced but not as efficiently as in-conjugation. Our study demonstrates that in-conjugation represents a significant fraction of the cytotoxic interaction. The results indicate that it may be a consequence of an actin polymerization and endonuclease activity dependent part of a cytotoxic mechanism.

Polarized and depolarized Raman spectra are obtained for a number of synthetic polynucleotides containing adenine, uracil, and thymine bases. The depolarization ratios are determined by two methods: (1) by dividing the -spectrum by the -spectrum and (2) after curve fitting. Overlapping bands, isotope splitting, reorientational broadening, and noncoincidence splitting affect the magnitude of the depolarization ratios over the band-width. For both Lorentz and Gauss curves these influences are simulated. A comparison of the Raman spectra of RNA and DNA molecules shows that the depolarization ratios for a number of similar base vibrations are different. The vibrational modes and the depolarization ratios of sugar vibrations are most sensitive to the structure of the polynucleotide. Base vibrations that have their potential energy distributed over base and sugar atoms also seem to be more sensitive to the structure. For instance the adenine vibrations at 1332 cm-1 and 1344 cm-1 in poly(dA), poly(dA) · poly(dT) and poly(dA-dT) · poly(dA-dT) have different depolarization ratios of, respectively, 0.36 and 0.28. This supports a previous assignment of the 1332 cm-1 band to a different sugar pucker (O4,-endo) than the C2,-endo corresponding with the 1344 cm-1 vibration. Assuming equal Raman scattering coefficients for this vibration, irrespective of the sugar pucker gives rise to the following ratio of the O4,-endo/C2,-endo in poly(dA) of 0.41, in poly(dA) · poly(dT) of 0.37, and in poly(dA-dT) · poly(dA-dT) of 0.41.

Changes in organization of F-actin during the cytotoxic process between NK and K562 cells have been observed and studied using confpcal laser scanning microscopy and quantitative fluorescence microscopy. An increase in F-actin content and orientation of F-actin towards the target cell have been observed in, conjugated NK cells. The increase in F-actin content probably reflects activation of the NK cell for the killing process. An increase in F-actin content in the conjugated K562 cell, occurring simultaneously with the appearance of filamentous actin structures that often originated/ended at the contact place with the NK cell, was also observed. These changes were delayed compared to the increase in F-actin content in the NK cell and were accompanied by increasing cytotoxic activity. This indicates that they were results of the interaction of the K562 cell with the activated NK cell. The possible role of target cell microfilaments in the cytotoxic process is addressed.

SDS-concentration-dependent alpha-synuclein structure: Upon interaction with SDS, alpha Syn folds into a structure with two antiparallel alpha-helices. We show from single-molecule FRET that alpha Synn adopts this conformation in an all-or-none fashion below the SDS critical micelle concentration. Population of the folded species is directly coupled to an increase in alpha-helix content; this suggests that the entire N terminus is involved in the transaction.

We have studied the interaction of the enzyme tissue transglutaminase (tTG), catalyzing cross-link formation between protein-bound glutamine residues and primary amines, with Parkinson's disease-associated alpha-synuclein protein variants at physiologically relevant concentrations. We have, for the first time, determined binding affinities of tTG for wild-type and mutant alpha-synucleins using surface plasmon resonance approaches, revealing high-affinity nanomolar equilibrium dissociation constants. Nanomolar tTG concentrations were sufficient for complete inhibition of fibrillization by effective alpha-synuclein cross-linking, resulting predominantly in intramolecularly cross-linked monomers accompanied by an oligomeric fraction. Since oligomeric species have a pathophysiological relevance we further investigated the properties of the tTG/alpha-synuclein oligomers. Atomic force microscopy revealed morphologically similar structures for oligomers from all alpha-synuclein variants; the extent of oligomer formation was found to correlate with tTG concentration. Unlike normal alpha-synuclein oligomers the resultant structures were extremely stable and resistant to GdnHCl and SDS. In contrast to normal beta-sheet-containing oligomers, the tTG/alpha-synuclein oligomers appear to be unstructured and are unable to disrupt phospholipid vesicles. These data suggest that tTG binds equally effective to wild-type and disease mutant alpha-synuclein variants. We propose that tTG cross-linking imposes structural constraints on alpha-synuclein, preventing the assembly of structured oligomers required for disruption of membranes and for progression into fibrils. In general, cross-linking of amyloid forming proteins by tTG may prevent the progression into pathogenic species.

We study adsorptive behaviour of biomolecules at the glass-solution interface in fluorescence correlation spectroscopy (FCS), and propose a negatively charged coating to eliminate the adsorption of molecules. In this article, we demonstrate confocal microscopic measurements on Cy3.5-90-mer-ssDNA and Cy3.5-90-bp-dsDNA in different solutions, and use two polymers – poly (acrylic acid, sodium salt) and poly (sodium 4-styrenesulfonate) to produce the negatively charged coating on glass coverslips. This technology enables more stable FCS measurements in extremely low concentration samples and reveals that the adsorptive behaviour of biomolecules is responsible for sudden disappearance of many iomolecules in low concentration solutions.

1D nanochannels are fabricated by direct bonding between the silicon wafer containing the nanochannels, microchannels, access holes and the blank thin glass of 170 µm thickness. The thin glass wafers are used as channel covers because of their appropriate thickness for use with coverglass corrected water immersion lenses. As the nanochannel chips are used on an inverted microscope, access holes are created in the silicon wafer so that polyimide is good selection for protection during deep etching of the macro holes. Fabricated nanochannels with 50 nm depth were successfully filled with low concentration of solutions Alexa 488 could be observed through fluorescence microscopy. These nanochannels are promising for mobility studies of single molecules such as quantum dots.