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At least 721 records · Page 40Linked to original sources
PubMed2007

Separation of sequences from host-pathogen interface using triplet nucleotide frequencies.

The identification of genes involved in host-pathogen interactions is important for the elucidation of mechanisms of disease resistance and host susceptibility. A traditional way to classify the origin of genes sampled from a pool of mixed cDNA is through sequence similarity to known genes from either the pathogen or host organism or other closely related species. This approach does not work when the identified sequence has no close homologues in the sequence databases. In our previous studies, we classified genes using their codon frequencies. This method, however, explicitly required the prediction of CDS regions and thus could not be applied to sequences composed from the non-coding regions of genes. In this study, we show that the use of sliding-window triplet frequencies extends the application of the algorithm to both coding and non-coding sequences and also increases the prediction accuracy of a Support Vector Machine classifier from 95.6+/-0.3 to 96.5+/-0.2. Thus the use of the triplet frequencies increased the prediction accuracy of the new method by more than 20% compared to our previous approach. A functional analysis of sequences detected gene families having significantly higher or lower probability to be correctly classified compared to the average accuracy of the method is described. The server to perform classification of EST sequences using triplet frequencies is available at (URL: http://mips.gsf.de/proj/est3).

Algorithms↗
PubMed2003

Effect of macromolecules and Triton X-100 on the triplet of aggregated chlorophyll in aqueous solution.

Chlorophyll a (Chla) in aqueous solution (2-6% acetone) is present as mono- and dihydrated aggregated forms which are characterized by specific ground state absorption spectra. The amount of dihydrated form is larger in the presence of macromolecules, such as bovine serum albumin (BSA), lysozime and polyvinyl alcohol (PVA), increasing from BSA to lysozime and PVA. Chla in aqueous acetone with and without macromolecules is characterized by low fluorescence and the absence of triplet-triplet (T-T) absorption. The ratio of dihydrated to monohydrated forms is significantly influenced by triton X-100. For lower triton X-100 concentrations, i.e. smaller than the critical micelle concentration of 0.26 mM (cmc), dihydrated forms are converted into monohydrated in both aqueous acetone and the presence of BSA or lysozime. In the presence of PVA dihydrated forms appeared to be resistant to triton X-100 action. Moreover, for triton X-100 concentrations of 2-3 times higher than cmc the amount of these forms is increased with time. T-T absorption of both mono- and dihydrated Chla aggregates was not detected in the presence of [triton X-100] < cmc. The lack of T-T absorption in aqueous acetone solution as well as in the presence of macromolecules implies that the triplet lifetime of the chlorophyll aggregates is short (tauT<10 ns) and/or the quantum yield of intersystem crossing is small (<5 x 10(-3)). The Chla monomers start to be formed as solubilized in the micelle for [triton X-100] larger than cmc, showing substantial fluorescence and T-T absorption.

Animals↗
PubMed2004

Selection for 3' end triplets for polymerase chain reaction primers.

The 3' end of a primer is a key component of PCR primer design. Many recommendations for the composition and sequence of the 3' end have been suggested based on theoretical considerations, but have not been verified experimentally. We analyzed 3' end triplets of PCR primer sequences obtained from refereed journal articles, to test those recommendations and to make empirical recommendations for primer design. The frequencies of the 64 possible 3'end triplets among 2137 PCR primers from the VirOligo database were not uniformly distributed. From the analysis, we found that unfavored and preferred 3' end triplets existed, and that the apparent preferences were not due to base compositions in viral genome sequences. Comparison of the sequences preferred by practitioners to those recommended, suggested that no single recommendation is entirely satisfactory. We suggest that recommendations be replaced with a scoring system incorporating empirical frequencies such as those reported here.

Base Composition↗
PubMedDate not supplied

HLA class I donor-specific triplet antibodies detected after renal transplantation.

The purpose of this study was to investigate whether IgG, non-donor-specific anti-HLA class I antibodies (HLAabI) detected after renal transplantation recognize immunogenic amino acid triplets expressed on the foreign graft. In addition, we sought to evaluate the effect of these antibodies as well as other posttransplant HLAabI on graft outcome. Posttransplant sera from 264 renal recipients were tested for the presence of IgG HLAabI and HLA class II-specific alloantibodies (HLAabII) by ELISA. The HLAMatchmaker computer algorithm was used to define the HLA class I non-donor-specific antibodies, which seem to recognize immunogenic amino acid triplets. Donor-specific triplet antibodies (DSTRab) were detected in 16 of 22 (72.7%) recipients based on at least one HLA-A or -B mismatched antigen with the donor. DSTRab were found either without (n = 7) or with (n = 9) HLA donor-specific antibodies (HLA-DSA). The presence of DSTRab alone in the periphery was associated with acute rejection, whereas the presence of both DSTRab and HLA-DSA was associated with chronic rejection and graft failure.

HLA-A Antigens↗
PubMed2003

Hyperfine structure of the photoexcited triplet state 3P680 in plant PS II reaction centres as determined by pulse ENDOR spectroscopy.

The triplet states in plant photosystem II (PS II), 3P680, and from chlorophyll a, 3Chl a, in organic solution have been investigated using pulse ENDOR combined with repetitive laser excitation at cryogenic temperature with the aim to obtain their hyperfine (hf) structure. The large zero field splitting (ZFS) tensor of 3P680 enabled orientation selection via the electron spin resonance (EPR) field setting along the ZFS tensor axes. ENDOR spectra have been obtained for the first time also for the in-plane X- and Y-orientations of the ZFS tensor. This allowed a full determination of the hf-tensors of the three methine protons and one methyl group of 3P680. Based on the orientations of the axes of these hf-tensors, a unique orientation of the axes of the ZFS tensor of 3P680 in the Chl a molecular frame was obtained. These data serve as a structural basis for determining the orientation of 3P680 in the PS II protein complex by EPR on single crystals (see M. Kammel et al. in this issue). The data obtained represent the first complete set of the larger hf-tensors of the triplet state 3P680. They reflect the spin density distribution both in the highest occupied (HOMO) and lowest unoccupied (LUMO) orbitals. The data clearly confirm that 3P680 is a monomeric Chl a species at low temperature (T=10 K) used, as has been proposed earlier based on D- and E-values obtained from EPR and optically detected magnetic resonance (ODMR) studies. Comparison with the hf data for the cation and anion radicals of Chl a indicates a redistribution of spin densities in particular for the LUMO orbital of the triplet states. The electron spin distribution in the LUMO orbital is of special interest since it harbours the excited electron in the excited P680 singlet state, from which light-induced electron transfer proceeds. Observed shifts of hf couplings from individual nuclei of 3P680 as compared with 3Chl a in organic solution are of special interest, since they indicate specific protein interactions, e.g. hydrogen bonding, which might be used in future studies for assigning 3P680 to a particular chlorophyll molecule in PS II.

Chlorophyll↗
PubMed1990

Reactions of excited triplet states of metal substituted myoglobin with dioxygen and quinone.

The triplet state absorption and phosphorescence of Zn and Pd derivatives of myoglobin were compared. Both metal derivatives exhibit long triplet state lifetimes at room temperature, but whereas the Pd derivative showed exponential decay and an isosbestic point in the transient absorption spectra, the decay of the Zn derivative was nonsingle exponential and the transient absorption spectra showed evidence of more than one excited state species. No difference was seen in triplet quenching by oxygen for either derivative, indicating that differences in the polypeptide chain between the two derivatives are not large enough to affect oxygen penetrability. Quenching was also observed by anthraquinone sulfonate. In this case, the possibility of long-range transfer by an exchange mechanism is considered.

Benzoquinones↗
PubMed1993

Excited states of tryptophan in cod parvalbumin. Identification of a short-lived emitting triplet state at room temperature.

The fluorescence and phosphorescence spectra of model indole compounds and of cod parvalbumin III, a protein containing a single tryptophan and no tyrosine, were examined in the time scale ranging from subnanoseconds to milliseconds at 25 degrees C in aqueous buffer. For both Ca- bound and Ca-free parvalbumin and for model indole compounds that contained a proton donor, a phosphorescent species emitting at 450 nm with a lifetime of approximately 20-40 ns could be identified. A longer-lived phosphorescence is also apparent; it has approximately the same absorption and emission spectrum as the short-lived triplet molecule. For Ca parvalbumin, the decay of the long-lived triplet tryptophan is roughly exponential with a lifetime of 4.7 ms at 25 degrees C whereas for N-acetyltryptophanamide in aqueous buffer the decay lifetime was 30 microseconds. In contrast, the lifetime of the long-lived tryptophan species is much shorter in the Ca-free protein compared with Ca parvalbumin, and the decay shows complex nonexponential kinetics over the entire time range from 100 ns to 1 ms. It is concluded that the photochemistry of tryptophan must take into account the existence of two excited triplet species and that there are quenching moieties within the protein matrix that decrease the phosphorescence yield in a dynamic manner for the Ca-depleted parvalbumin. In contrast, for Ca parvalbumin, the tryptophan site is rigid on the time scale of milliseconds.

Animals↗
PubMed1997

A model for the [C+-GxC]n triple helix derived from observation of the C+-GxC base triplet in a crystal structure.

A molecular modelling study on the [C+-GxC]n triple helix is reported. We have observed the C+-GxC base triplet in the crystal structure of an oligonucleotide-drug complex, between the minor-groove drug netropsin and the decanucleotide d(CGCAATTGCG)2. The complex was crystallised at pH 7.0, but the crystal structure, at a resolution of 2.4 A, shows that a terminal cytosine has become protonated and participates in a parallel C+-GxC base triplet. The structure of this triplet and its associated sugar-phosphate backbones have been energy-refined and then used to generate a triple helix. This has characteristics of the B-type family of DNA structures for two strands, with the third, the C+ strand, having backbone conformations closer to the A family.

DNA↗
PubMed2002

Neurofilament triplet proteins are restricted to a subset of neurons in the rat neocortex.

The cellular localisation of neurofilament triplet subunits was investigated in the rat neocortex. A subset of mainly pyramidal neurons showed colocalisation of subunit immunolabelling throughout the neocortex, including labelling with the antibody SMI32, which has been used extensively in other studies of the primate cortex as a selective cellular marker. Neurofilament-labelled neurons were principally localised to two or three cell layers in most cortical regions, but dramatically reduced labelling was present in areas such as the perirhinal cortex, anterior cingulate and a strip of cortex extending from caudal motor regions through the medial parietal region to secondary visual areas. However, quantitative analysis demonstrated a similar proportion (10-20%) of cells with neurofilament triplet labelling in regions of high or low labelling. Combining retrograde tracing with immunolabelling showed that cellular content of the neurofilament proteins was not correlated with the length of projection. Double labelling immunohistochemistry demonstrated that neurofilament content in axons was closely associated with myelination. Analysis of SMI32 labelling in development indicated that content of this epitope within cell bodies was associated with relatively late maturation, between postnatal days 14 and 21. This study is further evidence of a cell type-specific regulation of neurofilament proteins within neocortical neurons. Neurofilament triplet content may be more closely related to the degree of myelination, rather than the absolute length, of the projecting axon.

Animals↗
PubMed2003

Tubulin superfamily: giving birth to triplets.

Two new studies show that e tubulin is required for centriole/basal body duplication in both Chlamydomonas and Paramecium, adding to the list of new tubulin family members specifically involved in forming the centriole triplet microtubules. The function of these triplets, and the precise role of e tubulin in triplet formation, remains unclear.

Animals↗
PubMed2000

Triplet-state energies and substituent effects of excited aroyl compounds in the gas phase.

Triplet-state energy values obtained from the gas phase are still scarce. In this study, the triplet-state energies of 58 aroyl compounds, introduced as gas chromatographic peaks at atmospheric pressure and typically 473 K, have been determined from the 0-0 bands of their n --> pi* type phosphorescence spectra in excited nitrogen. Correlations of those gas-phase triplet-state energies with Hammett constants could be observed for substituted acetophenones, benzaldehydes and benzophenones.

Acetophenones↗
PubMed2002

Triplet-state photoexcitation dipole-jump relaxation method to observe adsorption/desorption kinetics at a reversed-phase silica/solution interface.

Electronic excitation of a probe chromophore can lead to a change in dipole moment that influences its activity or solubility in solution and changes its relative affinity for partitioning between two phases. Photoexcitation of a probe molecule can, therefore, perturb a sorption equilibrium, and the relaxation kinetics of the probe to the new equilibrium conditions can be monitored in a time-resolved luminescence experiment. The adsorption/desorption kinetics of rose bengal, distributed between a C-18 derivatized porous-silica surface and a liquid mobile-phase solution, were investigated. These kinetics were determined by observing their effect on the phosphorescence decay of the triplet state of rose bengal and its quenching by ferricyanide. The methanol/water solvent compositions were varied to alter the fraction of adsorbed rose bengal. The adsorption rate constant for the triplet state was determined from the dependence of the phosphorescence relaxation rate on dye concentration in solution. The results indicate that the adsorption kinetics are diffusion controlled and that the relaxation is influenced by efficient triplet-energy transfer between excited- and ground-state rose bengal at the C-18 silica/solution interface.

Journal Article↗
PubMed1993

Characterization of chlorophyll triplet promoting states in photosystem II sequentially induced during photoinhibition.

It has recently been demonstrated that strong illumination under anaerobic conditions leads to the double reduction of the primary quinone acceptor, QA, which in turn promotes the light-induced formation of triplet reaction center chlorophyll, 3P680, a potentially dangerous species to its protein surroundings in the presence of oxygen [Vass, I., Styring, S., Hundal, T., Koivuniemi, A., Aro, E.-M., & Anderson, B. (1992) Proc. Natl. Acad. Sci. U.S.A. 89, 1408-1412]. Here we have studied in further detail the formation of 3P680 producing centers in anaerobically photoinhibited photosystem II membranes by using low-temperature EPR spectroscopy. The results show that 3P680 formation occurs in three different populations of modified photosystem II centers. After a short period of photoinhibitory illumination, a very stable form of singly reduced QA is observed, with a decay halftime of several minutes at room temperature, and our results indicate that already this population of centers promotes the light-induced formation of the spin-polarized EPR signal from 3P680. The formation of these centers is enhanced below pH 6.0, indicating the involvement of a protonation event in neutralizing the negative charge on QA-, a prerequisite for efficient primary charge separation and subsequent triplet formation via the radical pair mechanism. If these centers are incubated in the dark, the stable singly reduced QA species is slowly reoxidized concomitant with the loss of its triplet forming ability. Extended photoinhibitory illumination converts the stable form of singly reduced QA to an EPR-silent species indicating the second reduction of QA-. The second negative charge on the double-reduced QA is neutralized most likely by a second protonation.(ABSTRACT TRUNCATED AT 250 WORDS)

Anaerobiosis↗
PubMed1984

Cooperative interactions in the system ribosomes-ribosomal protein S1-polynucleotide triplets.

Association equilibria have been determined in the ternary system uridyl triplets (T)-ribosomal protein S1 (S)-ribosomes (Rb) depleted of S1 at 6 and 10 mM Mg2+. For 1:1 stoichiometry of reactants, four thermodynamically independent equilibria characterize the ternary system. The binary interaction Rb + T was studied by following the fluorescence quenching of labeled ribosomes by added T. The Rb + T association constant for UpUpUp triplets was 10-20-fold greater than for ApUpG triplets. The interaction Rb + S was studied by following the changes in fluorescence anisotropy when labeled S1 reacted with ribosomes. The remaining two independent equilibrium constants (for S + T and RbT + S) were obtained from fits to observed anisotropy measurements when varying amounts of T were added to a solution of ribosomes and fluorescently labeled S1. This indirect procedure allows one to measure S + T binding, an association that is difficult to determine directly. Over the concentration interval 5-10 mM Mg2+, the association constant for Rb + S increases with the sixth power of [Mg2+], whereas the association constant for S + T decreases approximately 2-fold as Mg2+ is increased from 6 to 10 mM Mg2+. T binds to Rb more tightly at 10 mM than at 6 mM Mg2+. When S1 is bound to Rb, however, at 10 mM Mg2+ the binding constant for T is decreased 10-fold and the Mg2+ dependence is reversed. These interactions can be described in terms of coupling free energies. For the ternary complex, three linearly independent coupling free energies can be written.(ABSTRACT TRUNCATED AT 250 WORDS)

Binding Sites↗
PubMed1985

Reactivities of tyrosine, histidine, tryptophan, and methionine in radical pair formation in flavin triplet induced protein nuclear magnetic polarization.

In order to check the validity of several basic assumptions of protein photochemically induced nuclear polarization (protein photo-CIDNP), we have investigated the quenching processes of the dye triplets by the side chains of tyrosine, histidine, and tryptophan in a variety of molecular systems and environments. The quenching (H atom or electron transfer) is the generating process of the triplet electron-spin-correlated radical pair, the evolution of which gives rise to nuclear polarization. At pH 7 the quenching of 10-(carboxyethyl)flavin triplets by tyrosine and tryptophan is almost diffusion controlled. Quenching by histidine is slower. We have also investigated the slow quenching (by electron transfer) by the side chains of methionine and could show that quenching by cysteine S derivatives is negligible. Quenching by tyrosine and histidine peptides and by the tyrosines of the pancreatic trypsin inhibitor protein is slightly slower than by free side chains. Quenching is strongly viscosity controlled, to be expected of a process requiring bimolecular contact. Reactivity trends at high viscosities resemble those observed in fluid aqueous solutions. Activation energies of quenching by tyrosine, tryptophan, and histidine are similar. No difference could be detected in the mechanism of quenching by these side chains. No fast static quenching was observed that could compete with the diffusional process.

Flavins↗
PubMed1988

Comparative triplet-state properties of the three tryptophan residues in bacteriophage T4 lysozyme and in the enzyme complex with methylmercury(II).

Triplet-state energies, zero-field splittings (ZFS), and total decay rate constants of the individual triplet-state sublevels of the tryptophan (Trp) residues located at positions 126, 138, and 158 in bacteriophage T4 lysozyme have been determined by using low-temperature phosphorescence and optical detection of magnetic resonance spectroscopy in zero applied magnetic field. An investigation of spectral and kinetic properties of individual Trp residues was facilitated by measurements on point-mutated proteins containing two Trp----Tyr substitutions. We find that the phosphorescence lifetime of the buried Trp-138 is considerably shorter than those of the solvent-exposed Trp residues. CH3HgII binding to cysteine residues in T4 lysozyme selectively perturbs the triplet state of Trp-158 by means of an external heavy-atom effect. In contrast with the previous observation of selective x-sublevel perturbation in the Trp-CH3Hg complex, the radiative character of the z sublevel (z is the out-of-plane axis) is selectively enhanced due to the heavy-atom perturbation of Trp-158. The observed pattern of radiative and total sublevel decay constants of the perturbed Trp is attributed to a special orientation of the Hg atom with respect to the indole plane.

Binding Sites↗
PubMed1989

Perturbation of tryptophan residues by point mutations in bacteriophage T4 lysozyme studied by optical detection of triplet-state magnetic resonance spectroscopy.

We have investigated perturbations of the triplet-state properties of Trp residues in bacteriophage T4 lysozyme caused by point mutations using low-temperature phosphorescence and optical detection of triplet-state magnetic resonance (ODMR) spectroscopy. Five temperature-sensitive mutants have been studied in detail. These include lysozymes with the point mutations Gln-105----Ala, Gln-105----Gly, Gln-105----Glu, Ala-146----Thr, and Trp-126----Gln. Changes in phosphorescence 0,0 band wavelength, intensity, the triplet-state zero-field splitting (ZFS), and the wavelength dependence of the ZFS were detected only from Trp-138 in each mutant. In the case of the Q105A mutation, the perturbations on Trp-138 have been ascribed to the combination of an increase in the polarizability of the environment and to the loss of hydrogen bonding of the enamine nitrogen of indole. For the Q105G mutation, we believe that Q is replaced by a solvent molecule in H bonding, leading to relatively small changes. In the Q105E mutation, the perturbation results largely from the introduction of a charged residue. In the case of the mutation A146T, the perturbation is associated with a local conformational change in which Trp-138 is shifted to a more solvent-exposed location. On the other hand, no significant spectroscopic changes in Trp-126 and Trp-158 were found in any of the mutants, suggesting that the perturbations are probably localized near Trp-138 for the mutations of positions 105 and 146. However, in the mutation W126Q, which occurs approximately 16 A away from Trp-138, significant changes of Trp-138 are detected, suggesting that the effects of this mutation are propagated over large distances.

Luminescent Measurements↗
PubMed1989

Sequence specificity of DNA cleavage by bis(1,10-phenanthroline)copper(I): effects of single base pair transitions on the cleavage of preferred pyrimidine-purine-pyrimidine triplets.

The cleavage of DNA restriction fragments by bis(1,10-phenanthroline)copper(I) [[(OP)2CuI]+] is sequence dependent: the trimer TAT is most strongly preferred, while the trimer TGT and tetramers TAAT, TAGT, and CAGT are strongly to moderately preferred [Veal, J. M., & R. L. (1988) Biochemistry 27, 1822-1827]. [(OP)2CuI]+ cleavage of a series of oligonucleotide duplexes of the type 5'-CCCTPyPuPyCCCC-3'/3'-GGGAPuPyPuGGGG-5' (Py = pyrimidine; Pu = purine) was examined to determine the effects of purine substituents in the central triplet on specificity. The relative cleavage rates of different PyPuPy triplets in oligomers were similar to those observed for restriction fragments. The undecamer duplex containing the trimer TAT (TTATC) was most preferentially cleaved, predominantly at the central adenosine and the adjacent 3'-thymidine. Duplexes differing from TTATC by a single A.T----G.C transition in the central triplet were cleaved at significantly reduced rates relative to TTATC, the order of preference being TAT greater than TGT greater than TAC greater than CAT. By contrast, duplexes differing from TTATC by a single A.T----I.C transition were cleaved at rates similar to those for TTATC when the transition occurred at the 5'-pyrimidine or central purine [i.e., C(.I)AT and TIT]. A duplex containing the trimer TAC(.I) was cleaved at a reduced rate similar to the duplex containing TAC(.G). The guanine 2-amino group at positions 1 and 2, but not position 3, of a 5'-PyPuPy-3' trimer is therefore implicated as a strong inhibitor of DNA binding by the copper-phenanthroline complex.(ABSTRACT TRUNCATED AT 250 WORDS)

Base Composition↗