Analogs of RGDVY and GRGD peptides inhibit Mycobacterium kansasii phagocytosis

Continuing our research on Mycobacteria kansasii phagocytosis inhibition, we have examined in that context three series of peptides derived from the RGDVY and GRGD sequences. It was found that the levels of the inhibitory activity depend on the amino acid composition as well as on the particular peptide sequence. Distinct inhibitory activity was found in the case of thymopentin (RKDVY), the active fragment of thymopoietin. In this case the Mycobacterium phagocytosis inhibition should be combined with general immunostimulatory activity of RKDVY peptide. Our examination of a series of GRGDV analogs with a successively prolonged oligo-Gly linker inserted into the peptide chain showed that the distance between the Arg and Asp residues required for such an activity should be about 9A.     

Voltammetry as a virtual potentiometric sensor in modelling of a metal-ligand system and refinement of stability constants. Part 4. An electrochemical study of NiII complexes with methylene diphosphonic acid

The Ni(II)-MDP-OH system (MDP=methylene diphosphonic acid) and stability constants of complexes formed at ionic strength 0.15M at 298K were established by direct current polarography (DCP) and glass electrode potentiometry (GEP). The final M-L-OH model could only be arrived to by employing recent concept of virtual potentiometry (VP). VP-data were generated from non-equilibrium and dynamic DC polarographic technique. The VP and GEP data were refined simultaneously by software dedicated to potentiometric studies of metal complexes. Species distribution diagrams that were generated for different experimental conditions employed in this work assisted in making the final choice regarding the metal-ligand model. The model established contains ML, ML(2), ML(OH) and ML(OH)(2) with stability constants, as logbeta, 7.94+/-0.02, 13.75+/-0.02, 12.04 (fixed value), and 16.75+/-0.05, respectively. It has been demonstrated that virtual potential must be used in modelling operations (predictions of species formed) when a polarographic signal decreases significantly due to the formation of polarographically inactive species (or formation of inert complexes). The linear free energy relationships that included stability constant logK(1) for Ni(II)-MDP established in this work together with other available data were used to predict logK(1) values for Sm(III) and Ho(III) with MDP. The logK(1) values for Sm(III)-MDP and Ho(III)-MDP were estimated to be 9.65+/-0.10 and 9.85+/-0.10, respectively.     

Directional surface plasmon-coupled emission from a 3 nm green fluorescent protein monolayer

High-sensitivity detection schemes are of great interest for a number of applications. Unfortunately, such schemes are usually high-cost. We demonstrate a low-cost approach to a high-sensitivity detection scheme based on surface plasmon-coupled emission (SPCE). The SPCE of a monomolecular layer of green fluorescent protein (GFP) is reported here. The protein was electrostatically attached to a thin, SiO(2)-protected silver film deposited on a quartz substrate. The visible, directional emission of GFP was observed at a sharp, well-defined angle of 47.5 degrees from the normal to the coupling prism, and the spectrum corresponded to that of GFP. The SPCE resulting from the reverse Kretschmann configuration showed a 12-fold enhancement over the free space fluorescence. The directional emission was 97% p-polarized. The directionality and high polarization can be coupled with the intrinsic spectral resolution of SPCE to be used in the design miniaturized spectrofluorometers. The observation of SPCE in the visible region of the spectrum from a monolayer of protein opens up new possibilities in protein-based sensing.     

A protein biosensor for lactate

Blood lactate is a clinically valuable diagnostic indicator. In this preliminary report we describe a protein biosensor for L-lactate based on beef heart lactate dehydrogenase (LDH). LDH was noncovalently labeled with 8-anilino-1-naphthalene sulfonic acid (ANS). The ANS-labeled LDH displayed an approximately 40% decrease in emission intensity upon binding lactate. This decrease can be used to measure the lactate concentration. The ANS-labeled LDH was further utilized in a new sensing format, polarization sensing, which is suitable for miniaturization to a point-of-care lactate monitor. However, temporal instability of beef heart LDH indicates the need for further protein engineering prior to development of a more robust lactate-sensing protein.     

Effect of disordered hemes on energy transfer rates between tryptophans and heme in myoglobin.

Our recent linear dichroism study of heme transitions (Gryczynski, Z., E. Bucci, and J. Kusba. 1993. Photochem. Photobiology. in press) indicate that heme cannot be considered a planar oscillator when it acts as an acceptor of radiationless excitation energy transfer from tryptophan. The linear nature of the heme absorption transition moment in the near-UV region implies a strong dependence of the transfer rate factors on the relative angular position of the heme and tryptophan, i.e., on the kappa 2 orientation parameter of the Förster equation. Using the atomic coordinates of SW myoglobin we have estimated the variation of kappa 2 parameter as a function of the heme absorption transition moment direction. The simulations proved that transfer is very efficient and anticipates lifetimes in the picosecond range. Also, they showed that transfer is very sensitive to rotations of the heme around its alpha-gamma-meso-axis, which may reduce the efficiency of transfer to almost zero values, producing lifetimes very similar to those of free tryptophan, in the nanosecond range. Comparisons between the lifetime values reported in the literature and those here estimated suggest that natural heme disorder, in which heme is rotated 180 degrees around its meso axis, is at the origin of the nanosecond lifetimes found in myoglobin systems.     

Combined effects of nitrogen enrichment, sulphur pollution and climate change on fen meadow vegetation N:P stoichiometry and biomass

Nitrogen (N) and sulphur (S) deposition, as well as altered soil moisture dynamics due to climate change can have large effects on fen meadow biogeochemistry and vegetation. Their combined effects may differ strongly from their separate effects, since each process affects different nutrients through different mechanisms. However, the impacts of these environmental problems are rarely studied in combination. We therefore investigated the separate and interactive effects of current levels of N- and S-deposition and changes in soil moisture dynamics on fen meadow vegetation. We focused on vegetation biomass and N:P stoichiometry, including access to soil P through root surface phosphatase activity, in a 3-year factorial addition experiment in an N-limited rich fen meadow in the Biebrza valley in Poland. We applied 29.5 kg N ha^?1 year^?1 and 32.1 kg S ha^?1 year^?1, which correspond to current deposition levels in Western Europe. Changes in soil moisture dynamics due to climate change were mimicked by amplified drying of the soil in summer. This level of N-deposition had limited effects on plant biomass production in this rich fen, despite low foliar N:P ratios that suggest N limitation. This level of S-deposition, however, resulted in decreased vegetation P-uptake and biomass. We also showed that increased summer drought resulted in considerable increases in vegetation biomass. We found no interactive effects on vegetation biomass or N:P stoichiometry, possibly as a result of the limited main effects of the separate processes.     

On the genetic and structural similarities between the squash seeds polypeptide trypsin inhibitors and wheat germ agglutinin

Summary In this report we propose the disulfide bridges alignment in the squash polypeptide trypsin inhibitors. The prediction is based on the extensive homology in the amino acid sequence between these inhibitors and a portion of the wheat germ agglutinin domains for which the position of the disulfide bridges are known.     

Metal-enhanced fluorescence immunoassays using total internal reflection and silver island-coated surfaces

We present a generic immunoassay platform that uses enhanced total internal reflection fluorescence in the proximity of silver island films (SIFs), a surface coating consisting of metal (silver) particles. This platform is used with a model immunoassay where a protein antigen, rabbit immunoglobulin G, was immobilized on the SIF-coated glass surface. The signal from a fluorescent dye-labeled anti-rabbit antibody binding to the surface antigen was detected; different color dyes have been tested. Close placement of the fluorophore to surface-bound silver nanostructures results in dramatic signal enhancement (up to 40-fold) on the SIFs as compared with the glass slides. Use of the total internal reflection mode of excitation has significant advantages (over classic front-face excitation) for practical assay development. The limited evanescent wave excitation volume makes it possible to minimize the background signal and use the immunoassay with no need for any washing steps.     

Conformations of the signal recognition particle protein Ffh from Escherichia coli as determined by FRET

The signal recognition particle (SRP) initiates the co-translational targeting of proteins to the plasma membrane in bacteria by binding to the N-terminal signal sequence emerging from the translating ribosome. SRP in Escherichia coli is composed of one protein, Ffh, and 4.5S RNA. In the present work, we probe the structure of Ffh alone and in the complex with 4.5S RNA by measuring distances between different positions within Ffh and between Ffh and 4.5S RNA by fluorescence resonance energy transfer (FRET). According to the FRET distances, NG and M domains in free Ffh are in close contact, as in the A/A arrangement in the crystal structure of Ffh from Thermus aquaticus, in agreement with the formation of a crosslink between cysteine residues at two critical positions in the G and M domains. Upon Ffh binding to 4.5S RNA or a 61 nucleotide fragment comprising internal loops A-C, the G and M domains move apart to assume a more open conformation, as indicated by changes of FRET distances. The movement is smaller when Ffh binds to a 49 nucleotide fragment of 4.5S RNA comprising only internal loops A and B, i.e. lacking the binding site of the NG domain. The FRET results suggest that in the SRP complex 4.5S RNA is present in a bent, rather than extended, conformation. The domain rearrangement of Ffh that takes place upon formation of the SRP is probably important for subsequent steps of membrane targeting, including interactions with the translating ribosome and the SRP receptor.     

Inexpensive Computation of the Inverse of the Genomic Relationship Matrix in Populations with Small Effective Population Size

Many computations with SNP data including genomic evaluation, parameter estimation, and genome-wide association studies use an inverse of the genomic relationship matrix. The cost of a regular inversion is cubic and is prohibitively expensive for large matrices. Recent studies in cattle demonstrated that the inverse can be computed in almost linear time by recursion on any subset of ∼10,000 individuals. The purpose of this study is to present a theory of why such a recursion works and its implication for other populations. Assume that, because of a small effective population size, the additive information in a genotyped population has a small dimensionality, even with a very large number of SNP markers. That dimensionality is visible as a limited number of effective SNP effects, independent chromosome segments, or the rank of the genomic relationship matrix. Decompose a population arbitrarily into core and noncore individuals, with the number of core individuals equal to that dimensionality. Then, breeding values of noncore individuals can be derived by recursions on breeding values of core individuals, with coefficients of the recursion computed from the genomic relationship matrix. A resulting algorithm for the inversion called “algorithm for proven and young” (APY) has a linear computing and memory cost for noncore animals. Noninfinitesimal genetic architecture can be accommodated through a trait-specific genomic relationship matrix, possibly derived from Bayesian regressions. For populations with small effective population size, the inverse of the genomic relationship matrix can be computed inexpensively for a very large number of genotyped individuals.