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It is shown for the first time that the measurement of triplet phases of three-beam cases where strong structure factors are involved is possible in small protein structures, for example myoglobin. The exploitation of the triplet phase from the interference profile is not affected as long as the structure factors of unavoidable overlapping three-beam cases are small.
Crystallization of a DNA double helix with overhanging bases at the 5'-ends of both strands, results in the formation of two crystallographically independent (C.G)*G triplets. In a previous report [Van Meervelt, Vlieghe, Dautant, Gallois, Précigoux & Kennard (1995). Nature (London), 374, 742-744] the unique molecular packing of the duplex and the Hoogsteen hydrogen-bond pattern and parallel backbone orientation of the guanine-containing strands in the triplets was described. The fine structural details and hydration of the d(GCGAATTCG) crystal structure refined to 2.05 A (R = 0.168, 86 water molecules, two Mg(2+) cations) are now presented. Helical parameters, stacking effects, the geometry at the duplex-triplex junction, and the hydration of the minor groove are discussed and compared with related theoretical and crystal structures.
The physical basis of the conditional probability distributions of the quartet and of the triplet are investigated by means of the 'Patterson' and 'modulus' sum functions, respectively. From this study, a new conditional probability distribution of the triplet follows which has been tested on real data from three structures of different size. The empirically found distribution is compared with Cochran's closely related distribution.
In a previous communication [Weckert et al. (1999). Acta Cryst. D55, 1320-1328], the feasibility of the measurement of a large set of triplet phases by three-beam interference was demonstrated. This paper reports the methodology for the calculation of an electron-density map from this limited amount of experimental phase information and the map's properties with respect to model building and refinement. The tetragonal form of hen egg-white lysozyme (HEWL) was chosen as a test structure for the development of this method. The quality of the electron-density map obtained from all measured triplet phases allows a straightforward and nearly complete interpretation. The starting model was refined to a final R value of 17.4%. In a second step, the minimum number of phased reflections needed for the interpretation of an electron-density map was investigated, applying criteria based on |F| and resolution.
Fragile X syndrome is caused by expansion of a d(CGG) triplet repeat in the 5'-untranslated region of the first exon of the FMR1 gene resulting in silencing of the gene. The d(CGG) repeat has been reported to form hairpin and quadruplex structures in vitro, and formation of these higher structures could be responsible for its unstable expansion in the syndrome, although molecular mechanisms underlying the repeat expansion still remain elusive. We have previously proved that UP1, a proteolytic product of hnRNP A1, unfolds the intramolecular quadruplex structures of d(GGCAG)5 and d(TTAGGG)4 and abrogates the arrest of DNA synthesis at d(GGG)n sites. Here, we demonstrate that the d(CGG) repeat forms a peculiar DNA structure, which deviates from the canonical B-form structure. In addition, UP1 was demonstrated by CD spectrum analysis to unfold this characteristic higher structure of the d(CGG) repeat and to abrogate the arrest of DNA synthesis at the site. This ability of UP1 suggests that unfolding of unusual DNA structures of a triplet repeat is required for DNA synthesis processes.
A calcium-dependent protease fully active with 0.2 mM Ca2+ was found associated with the neurofilament-enriched cytoskeleton of the rat spinal cord prepared by the treatment with Triton X-100. The enzyme preferentially degrades the 160-kDa component of the neurofilament triplet. In addition, a soluble calcium-dependent protease activity was found in the supernatant from the spinal cord, which degraded a variety of cytoskeletal proteins including the neurofilament triplet, glial fibrillary acidic (GFA) protein, actin, tubulin, and a high molecular weight protein associated with microtubules. The possibility that the cytoskeleton-bound activity is an artefactual association of the soluble enzyme to the cytoskeleton seems to be negated on the basis of the following dissociation and reassociation experiments. The protease activity remained associated with the cytoskeleton in the physiological ionic strength, and was not completely dissociated from it until the KC1 concentration was raised to 0.6 M. When the 0.6 M KCl-extract was dialysed against salt-free buffer to remove KC1, and added back to the protease-free cytoskeletal pellet, proteolytic activity was partially restored. Full activity returned only when the extract and the protease-free cytoskeletal pellet were first combined in the presence of 0.6 M KC1, and then slowly reassociated by dialysis against salt-free buffer. Dissociated enzyme was rapidly inactivated at 37 degrees C in the presence of Ca2+. These results suggest the structural association of the protease with the cytoskeleton under the physiological condition.
Maternal serum alpha-fetoprotein (AFP) levels were higher in six triplet pregnancies and three quadruplet pregnancies than in control singleton pregnancies matched for maternal age, parity and time of gestation at which the serum sample was taken. Between 12 and 23 weeks of pregnancy, the average AFP levels among the triplet pregnancies was three times that found in the singleton pregnancies, and the level in the quadruplet pregnancies was even higher. Maternal serum AFP levels appear to be associated with the number of fetuses in utero.
Intact neurofilaments were isolated from bovine spinal cord white matter, washed by sedimentation in 0.1 M-NaCl, and extracted with 8 M-urea. Solubilized neurofilament triplet proteins of molecular weights approximately 68,000 (P68), 150,000 (P150), and 200,000 (P200) were purified by preparative electrophoresis, using an LKB 7900 Uniphor apparatus. The method provides for an enhanced yield of purified protein and has markedly reduced admixture of electrophoresed protein with acrylamide and associated protein contaminants. Amino acid compositions of the purified neurofilament triplet proteins are reported and compared.
One of the pathological changes of Alzheimer's disease is the deposit of beta/A4 protein, which is derived from Alzheimer amyloid precursor protein (APP). In the secretory pathway, APP is cleaved at an internal region of beta/A4 protein by a hypothetical enzyme "secretase." Our previous study showed that the site of cleavage of APP by secretase is determined by the length from the membrane-spanning region. To investigate the role of the transmembrane region in APP secretion, we constructed the mutations of triplet lysine residues (Lys724-Lys725-Lys726), which are located just in the carboxyl region after the proposed membrane domain. The mutations were as follows: VVK, Val724-Val725-Lys726; LLI, Leu724-Leu725-Ile726; and EEE, Glu724-Glu725-Glu726. Wild-type APP and mutant APPs were expressed transiently in COS-1 cells by cDNA transfection. The hydrophobic mutant VVK and LLI were processed and secreted in a way similar to that of the wild-type APP, although the rate of secretion was decreased. The acidic mutant EEE was not secreted into medium. Proteinase K treatment and cell surface biotinylation of the COS-1 cells expressing APP revealed that APP was located in the plasma membrane with a short intracellular carboxyl region. However, EEE was completely digested by proteinase K treatment, which suggested that the whole residues of this mutant are located at the outer surface of the cell, including its proposed membrane domain and carboxyl region. This mutant was not cleaved at all by secretase. These findings suggested that the triplet lysine residues of AP after the predicted membrane spanning domain play an important role in the membrane anchorage.(ABSTRACT TRUNCATED AT 250 WORDS)
Kennedy-Alter-Sung (KAS) disease in a hereditary lower motor neuron disease. In this study, we investigate 2 KAS patients presenting with progressive muscle weakness and wasting, action tremor, perioral fasciculation and gynecomastia. Three carriers and 5 healthy members from this 3-generation KAS Chinese family and 60 normal Chinese controls were included in this study. Hormone studies revealed normal serum level in thyrotropin, prolactin, testosterone, leuteinizing hormone, follicle stimulating hormone, and estradiol. Lipid study disclosed type IV hyperlipoproteinemia in 2 KAS patients and 3 healthy members. Molecular studies revealed that the number of CAG triplet repeats in the first exon of androgen receptor gene of the normal allele is in the range of 15-19 and 12-25 in this family and normal controls, respectively. However, the number of CAG repeat of androgen receptor gene were unstable in the mutant alleles with a range of 41-45 and increased from generation to generation (genomic anticipation) in the 2 KAS patients and 3 female carriers. We conclude that the CAG triplet repeats in mutant allele were unstable in the family with the KAS disease. Furthermore, type IV hyperlipoproteinemia may be a co-transmitted syndrome in the family with KAS disease.
Human plasma-derived von Willebrand factor (hp-vWF) and recombinant von Willebrand factor (r-vWF) have been fractionated by heparin affinity chromatography followed by multimer analysis using SDS-agarose gel electrophoresis. Because heparin binding sites are contained in each vWF subunit, high molecular weight multimers of r-vWF and hp-vWF, respectively, were eluted with higher salt concentration, in comparison to r-vWF and hp-vWF molecules with a low degree of multimerization. Heparin affinity chromatography did not affect the multimer composition of r-vWF. By contrast, faster migrating satellite bands and slower migrating satellite bands of hp-vWF exhibited reduced and increased heparin affinity, respectively, compared to the intermediate band of the same triplet. Because heparin binding sites are localised in the N-terminal domain of the hp-vWF subunit, this result confirms a structural model of hp-vWF (Fischer et al., Biochem. J. 1998;331:483-488) suggested recently, in which the slower migrating satellite bands have excess of one N-terminal fragment and the faster migrating satellite bands lack one N-terminal fragment, respectively, in comparison with the corresponding intermediate triplet band.
Phosphophoryns (PPs) are unique aspartic acid and phosphoserine-rich proteins present in all species of dentin. Rat incisor odontoblast cDNA libraries contain messages encoding several acidic phosphorylated, serine-rich proteins. At least two of these share a common C-terminal domain coding region sequence. The polypeptide sequences in the N-terminal direction immediately adjacent to the conserved C-terminal domains of these two proteins (DMP2, DMP3) are distinctly different. In this domain, the DMP2 has extensive sequences of (DSS)n repeats with n as large as 24. DMP3 has fewer and shorter triplet sequences, n = 3, 4. The major rat incisor PPs (90-95 kDa) probably have the (DSS)n>>3. We propose that the name phosphophoryn be reserved for the extracellular matrix proteins with these extended repeats. DMPI, although strongly acidic, does not fit this category. If the S residues are phosphorylated and n > 3, conformational energy minimization computations show the (DSS)n sequence to assume a unique extended structure with parallel arrays of carboxylate and phosphate groups which may function as Ca2+ ion interaction edges. The phosphorylation of recombinant DMP2 C-terminal domain by various kinases has been examined. The repeat domains are not direct substrates for the CK2-like kinases but the kinases act in concert, so that the phosphorylation is hierarchical, apparently controlled by the presence of specific interruptions between the triplet domains.
This paper describes the phosphorescence emission and decay times of NAD+ and its fluorescent etheno derivative, epsilon-NAD+, in the pyrazole ternary complex with horse liver alcohol dehydrogenase (ADH). We show that the epsilon-NAD+ triplet state, as well as the tryptophan triplet state, can be utilized to monitor the coenzyme-enzyme interaction. The decays of NAD+ and AMP are single exponential, and the lifetimes are the same within experimental error. The phosphorescence lifetimes, evaluated as single exponentials, are slightly shorter in epsilon-NAD+ than they are in epsilon-AMP. Whereas the decay of epsilon-AMP was adequately fit by a single exponential with a time constant of very close to 0.5 s, it was necessary to fit the decay of epsilon-NAD+ to a double exponential. Ternary complexes with NAD+ excited at 297 nm exhibit decay kinetics nearly identical to those of ADH by itself. On the other hand, when excitation of the epsilon-NAD+ ternary complex is provided at 313 nm, where there is very little absorption by either tryptophan residue, the decay law of the ternary complex is similar to that of epsilon-NAD+ in solution. Our results demonstrate that NAD+ and epsilon-NAD+ quench tryptophan phosphorescence in ADH. Normalizing the phosphorescence intensity to the 0-0 vibronic band assigned to Trp-15 (blue-edge), we calculate a 21% decrease in the phosphorescence associated with Trp-314 at stoichiometric saturation of the coenzyme binding sites with NAD+ in the ternary complex. When the active sites are saturated with epsilon-NAD+, the relative phosphorescence due to Trp-314 decreases by 63%.(ABSTRACT TRUNCATED AT 250 WORDS)
Laser photolysis techniques have been used to characterize the reactivity of triplet state lipoidal benzophenone derivatives toward fatty acids and glycerides in benzene solution. The reactivities of benzophenone-4-heptyl-4'-pentanoic acid (BHPA) toward fatty acid compounds having different configurations of olefinic bonds have been determined. The rates of hydrogen abstraction are found to be lower when compared with similar measurements using benzophenone alone. However, the contribution of physical quenching of the triplet derivative by double bonds also appears to be slightly lower than that found with benzophenone itself. The hydrogen abstraction efficiencies of three other benzophenone derivatives toward linoleic acid in benzene have also been measured. For benzophenone incorporated into a fatty acid molecule, there is a limited relationship between structure and photoreactivity. Finally, these sensitizers have been incorporated into mixed SDS/linoleate micelles to determine the effects of molecular organization on photochemical behavior of the sensitizer and lipid.
The mechanism of the photoreceptor acting on the circadian conidiation rhythm of Neurospora crassa was studied, with the following results: (1) the efficiency of 8-haloflavins as sensitizers increased with their triplet yields. (2) Phase shifts were not abolished by removal of oxygen prior to illumination. (3) Oxygen inhibited phase shifts when introduced into the cultures after light treatment. It is proposed that the blue light photoreceptor for the circadian clock of Neurospora crassa acts (1) from its triplet state, but (2) not via singlet oxygen; (3) signal transduction involves (an) oxygen-sensitive intermediate(s).
The singlet and triplet states of the anthralin (1,8-dihydroxy-9-anthrone) dehydrodimer have been produced selectively in benzene via pulsed laser excitation and pulse radiolysis respectively. The lifetime of S1 is less than or equal to 30 ps, that of T1 short but unspecified. Both states fragment spontaneously to yield a pair of anthralin radicals. The singlet radical pair predominantly undergoes geminate recombination within the solvent cage. In contrast, the corresponding triplet radical pair undergoes essentially exclusive cage escape to give the anthralin free radical (lambda max 370, 490 and 720 nm) which recombines under normal diffusive conditions. Both recombination processes lead, at least in part, to one or more species which have been assigned as tautomeric forms of the original dimer. The anthralin free radical in benzene is insensitive to the vitamin E model 6-hydroxy-2,2,5,7,8-pentamethylchroman and reacts only slowly with oxygen.
A photoacoustic (PA) effect theory taking into account two heat sources corresponding to the radiationless relaxation processes of two states of different lifetimes and to the heat diffusion across the sample is herewith presented. Results obtained demonstrate that the amplitude and the phase of the PA signal depend on the sample's thermal properties, on its optical absorption coefficient, on the lifetime of the long-lived excited state, and on the ratio of the two heat sources. This ratio can be expressed as a function of the product of the energy of the excited state times the quantum yield of its production. Simulations of PA amplitude and phase variations vs light modulation frequency exhibit new features of the PA signal:phase inversion and fast decrease of the amplitude. Experimental verifications were carried out on solutions and gels. Fitting of the amplitude and phase variations allow us to measure the lifetime and conversion yield of the intermediate state which can be a triplet state or singlet oxygen, O2(1 delta g). The addition of an acceptor, specific to O2(1 delta g), induces changes in the amplitude of the PA signal which can be used to study the production and deactivation of this excited form of oxygen. This work demonstrates the usefulness of PA in the detection of metastable excited states such as the triplet state and singlet oxygen and in their quantitative analysis.
We have labeled rabbit skeletal muscle actin with the triplet probe erythrosin-5-iodoacetamide and characterized the labeled protein. Labeling decreased the critical concentration and lowered the intrinsic viscosity of F-actin filaments; labeled filaments were motile in an in vitro motility assay but were less effective than unlabeled F-actin in activating myosin S1 ATPase activity. In unpolymerized globular actin (G-actin), both the prompt and delayed luminescence were red-shifted from the spectra of the free dye in solution and the fluorescence anisotropy of the label was high (0.356); filament formation red shifted all excitation and emission spectra and increased the fluorescence anisotropy to 0.370. The erythrosin phosphorescence decay was at least biexponential in G-actin with an average lifetime of 99 microseconds while in F-actin the decay was approximately monoexponential with a lifetime of 278 microseconds. These results suggest that the erythrosin dye was bound at the interface between two actin monomers along the two-start helix. The steady-state phosphorescence anisotropy of F-actin was 0.087 at 20 degrees C and the anisotropy increased to approximately 0.16 in immobilized filaments. The phosphorescence anisotropy was also sensitive to binding the physiological ligands phalloidin, cytochalasin B and tropomyosin. This study lays a firm foundation for the use of this triplet probe to study the large-scale molecular dynamics of F-actin.