Gamma-Ray and Radio-Frequency Radiation from Thunderstorms Observed from Space and Ground

Terrestrial gamma ray flashes (TGFs) are a class of enigmatic electrical discharges in the Earth’s atmosphere. In this study, we analyze an unprecedentedly large dataset comprised of 2188 TGFs whose signatures were simultaneously measured using space- and ground-based detectors over a five-year period. The Gamma-ray Burst Monitor (GBM) on board the Fermi spacecraft provided the energetic radiation measurements. Radio frequency (RF) measurements were obtained from the Global Lightning Dataset (GLD360). Here we show the existence of two categories of TGFs − those that were accompanied by quasi-simultaneous electromagnetic pulses (EMPs) detected by the GLD360 and those without such simultaneous EMPs. We examined, for the first time, the dependence of the TGF-associated EMP-peak-amplitude on the horizontal offset distance between the Fermi spacecraft and the TGF source. TGFs detected by the GBM with sources at farther horizontal distances are expected to be intrinsically brighter and were found to be associated with EMPs having larger median peak-amplitudes. This provides independent evidence that the EMPs and TGFs are produced by the same phenomenon, rather than the EMPs being from “regular” lightning in TGF-producing thunderstorms.

A gamma-ray burst with a high-energy spectral component inconsistent with the synchrotron shock model

Gamma-ray bursts are among the most powerful events in nature. These events release most of their energy as photons with energies in the range from 30 keV to a few MeV, with a smaller fraction of the energy radiated in radio, optical, and soft X-ray afterglows. The data are in general agreement with a relativistic shock model, where the prompt and afterglow emissions correspond to synchrotron radiation from shock-accelerated electrons. Here we report an observation of a high-energy (multi-MeV) spectral component in the burst of 17 October 1994 that is distinct from the previously observed lower-energy gamma-ray component. The flux of the high-energy component decays more slowly and its fluence is greater than the lower-energy component; it is described by a power law of differential photon number index approximately -1 up to about 200 MeV. This observation is difficult to explain with the standard synchrotron shock model, suggesting the presence of new phenomena such as a different non-thermal electron process, or the interaction of relativistic protons with photons at the source.

Synthesis and study of the fluorescein conjugate of the nucleotide dPTP

The synthesis of a fluorescein conjugate on the non-natural base P is described. The ability of the newly synthesised fluorescein--dPTP and of a fluorescein-11-dUTP to compete with the natural nucleotide TTP was also studied. Overall the efficiency of labelling a nucleic acid with a fluorescein moiety was found to be approximately equal.

Statistical Properties of SGR 1806-20 Bursts

We present statistics of SGR 1806-20 bursts, combining 290 events detected with the Rossi X-Ray Timing Explorer/Proportional Counter Array, 111 events detected with the Burst and Transient Source Experiment, and 134 events detected with the International Cometary Explorer. We find that the fluence distribution of bursts observed with each instrument are well described by power laws with indices 1.43, 1.76, and 1.67, respectively. The distribution of time intervals between successive bursts from SGR 1806-20 is described by a lognormal function with a peak at 103 s. There is no correlation between the burst intensity and either the waiting times until the next burst or the time elapsed since the previous burst. In all these statistical properties, SGR 1806-20 bursts resemble a self-organized critical system, similar to earthquakes and solar flares. Our results thus support the hypothesis that the energy source for soft gamma repeater bursts is crustquakes due to the evolving, strong magnetic field of the neutron star, rather than any accretion or nuclear power.

Hard Burst Emission from the Soft Gamma Repeater SGR 1900+14

We present evidence for burst emission from SGR 1900+14 with a power-law high-energy spectrum extending beyond 500 keV. Unlike previous detections of high-energy photons during bursts from soft gamma repeaters (SGRs), these emissions are not associated with extraordinarily bright flares. Not only is the emission hard, but the spectra are better fitted by D. Band's gamma-ray burst (GRB) function rather than by the traditional optically thin thermal bremsstrahlung model. We find that the spectral evolution within these hard events obeys a hardness/intensity anticorrelation. Temporally, these events are distinct from typical SGR burst emissions in that they are longer ( approximately 1 s) and have relatively smooth profiles. Despite a difference in peak luminosity of greater, similar1011 between these bursts from SGR 1900+14 and cosmological GRBs, there are striking temporal and spectral similarities between the two kinds of bursts, aside from spectral evolution. We outline an interpretation of these events in the context of the magnetar model.

Statistical Properties of SGR 1900+14 Bursts

We study the statistics of soft gamma repeater (SGR) bursts using a database of 187 events detected with BATSE and 837 events detected with the Rossi X-Ray Timing Explorer Proportional Counter Array; all events are from SGR 1900+14 during its 1998-1999 active phase. We find that the fluence or energy distribution of bursts is consistent with a power law of index 1.66, over 4 orders of magnitude. This scale-free distribution resembles the Gutenberg-Richter law for earthquakes and gives evidence for self-organized criticality in SGRs. The distribution of time intervals between successive bursts from SGR 1900+14 is consistent with a lognormal distribution. There is no correlation between burst intensity and the waiting times till the next burst, but there is some evidence for a correlation between burst intensity and the time elapsed since the previous burst. We also find a correlation between the duration and the energy of the bursts, but with significant scatter. In all these statistical properties, SGR bursts resemble earthquakes and solar flares more closely than they resemble any known accretion-powered or nuclear-powered phenomena. Thus, our analysis lends support to the hypothesis that the energy source for SGR bursts is internal to the neutron star and plausibly magnetic.

Synthesis and RNA polymerase incorporation of the degenerate ribonucleotide analogue rPTP

The synthesis and enzymatic incorporation into RNA of the hydrogen bond degenerate nucleoside analogue 6-(beta-d-ribofuranosyl)-3, 4-dihydro-8H-pyrimido[4,5-c]-[1,2]oxazin-7-one (P) is described. The 5'-triphosphate of this analogue is readily incorporated by T3, T7 and SP6 RNA polymerases into RNA transcripts, being best incorporated in place of UTP, but also in place of CTP. When all the uridine residues in an HIV-1 TAR RNA transcript are replaced by P the transcript has similar characteristics to the wild-type TAR RNA, as demonstrated by similar melting temperatures and CD spectra. The P-substituted TAR transcript binds to the Tat peptide ADP-1 with only 4-fold lowered efficiency compared with wild-type TAR.

Hydrogen exchange in native and alcohol forms of ubiquitin

Ubiquitin adopts a non-native folded structure in 60% methanol solution at low pH. Two-dimensional nuclear magnetic resonance (2D NMR) was used to measure the hydrogen-exchange rates of backbone amide protons of ubiquitin in both native and methanol forms, and to characterize the structure of ubiquitin in the methanol state. Protection factors (the ratios of experimentally determined exchange rates to the rates calculated for an unfolded polypeptide) for protons in the native form of ubiquitin range from less than 10 to greater than 10(5). Most of the protons that are protected from exchange are located in regions of hydrogen-bonded secondary structure. The most strongly protected backbone amide protons are those of residues comprising the hydrophobic core. Hydrogen exchange from ubiquitin in methanol solution was too rapid to measure directly by 2D NMR, so a labeling scheme was employed, in which exchange with solvent occurred while the protein was in methanol solution. Exchange was quenched by dilution with aqueous buffer after the desired labeling time, and proton occupancies were measured by 1H NMR of the native form of the protein. Protection factors for protons in the methanol form of ubiquitin range from 2.6 to 42, with all protected protons located in hydrogen-bonded structure in the native form. Again, the most strongly protected protons are those of residues in the hydrophobic core. Comparison of the patterns of the hydrogen-exchange rates in the native and methanol forms indicates that almost all of the native secondary structure persists in the methanol form, but that it is almost uniformly destabilized by 4-6 kcal/mol.(ABSTRACT TRUNCATED AT 250 WORDS)

Early hydrogen-bonding events in the folding reaction of ubiquitin

The formation of hydrogen-bonded structure in the folding reaction of ubiquitin, a small cytoplasmic protein with an extended beta-sheet and an alpha-helix surrounding a pronounced hydrophobic core, has been investigated by hydrogen-deuterium exchange labeling in conjunction with rapid mixing methods and two-dimensional NMR analysis. The time course of protection from exchange has been measured for 26 back-bone amide protons that form stable hydrogen bonds upon refolding and exchange slowly under native conditions. Amide protons in the beta-sheet and the alpha-helix, as well as protons involved in hydrogen bonds at the helix/sheet interface, become 80% protected in an initial 8-ms folding phase, indicating that the two elements of secondary structure form and associate in a common cooperative folding event. Somewhat slower protection rates for residues 59, 61, and 69 provide evidence for the subsequent stabilization of a surface loop. Most probes also exhibit two minor phases with time constants of about 100 ms and 10 s. Only two of the observed residues, Gln-41 and Arg-42, display significant slow folding phases, with amplitudes of 37% and 22%, respectively, which can be attributed to native-like folding intermediates containing cis peptide bonds for Pro-37 and/or Pro-38. Compared with other proteins studied by pulse labeling, including cytochrome c, ribonuclease, and barnase, the initial formation of hydrogen-bonded structure in ubiquitin occurs at a more rapid rate and slow-folding species are less prominent.

Functional and nonfunctional LamB signal sequences can be distinguished by their biophysical properties

The role of the signal sequence in the secretion of proteins remain unclear despite extensive research. We have examined properties of synthetic peptides corresponding to a family of signal sequences derived from the lamB gene of Escherichia coli, including five examples of known phenotype that contain mutations in the signal sequence. By circular dichroism spectroscopy, the wild type and export-component mutant signal peptides show a high alpha-helix content in membrane mimetic environments (sodium dodecyl sulfate micelles and phospholipid vesicles). Tendency to adopt helical conformations is clearly not sufficient to define a functional signal sequence, however, as some nonfunctional mutant signal peptides also contain a relatively high proportion of alpha-helix. The affinity of these peptides for phospholipid monolayers as assessed by surface tensiometry reveals further distinguishing properties. Export-competent peptides show an increased affinity for and greater perturbation of phospholipid monolayers and bilayers than to export-defective peptides. These results suggest a lipid binding role for the signal sequence during protein export in addition to its recognition by proteins of the export pathway.

Conformations and orientations of a signal peptide interacting with phospholipid monolayers

The interaction of a chemically synthesized 25-residue signal peptide of LamB protein from Escherichia coli with phospholipids has been studied with a film balance technique. The conformation, orientation, and concentration of the peptides in lipid monolayers have been determined from polarized infrared spectroscopy, ultraviolet spectroscopy, and assay of 14C-labeled peptide in transferred films. When the LamB signal peptide is injected into the subphase under a phosphatidylethanolamine-phosphatidylglycerol monolayer at low initial pressure, insertion of a portion of the peptide into the lipid film is evidenced by a rapid rise in film pressure. Spectroscopic results obtained on films transferred to quartz plates and Ge crystals show that the peptide is a mixture of alpha-helix and beta-conformation where the long axis of the alpha-helix penetrates the monolayer plane and the beta-structure is coplanar with the film. By contrast, when peptide is injected under lipid at high initial pressure, no pressure rise is observed, and the spectroscopic results show the presence of only beta-structure which is coplanar with the monolayer. The spectroscopic and radioassay results are all consistent with the picture of a peptide anchored to the monolayer through electrostatic binding with a helical portion inserted into the lipid region of the monolayer and a beta-structure portion resident in the aqueous phase. The negative charges on the lipid molecules are roughly neutralized by the positive charges of the peptide.

Protein translocation into Escherichia coli membrane vesicles is inhibited by functional synthetic signal peptides

A synthetic peptide corresponding to the signal sequence of wild type Escherichia coli lambda-receptor protein (LamB) inhibits in vitro translocation of precursors of both alkaline phosphatase and outer membrane protein A into E. coli membrane vesicles (half-maximal inhibition at 1-2 microM). By contrast, the inhibitory effect was nearly absent in a synthetic peptide corresponding to the signal sequence from a mutant strain that harbors a deletion mutation in the LamB signal region and displays an export-defective phenotype for this protein in vivo. Two peptides derived from pseudorevertant strains that arose from the deletion mutant and exported LamB in vivo were found to inhibit in vitro translocation with effectiveness that correlated with their in vivo export ability. Controls indicated that these synthetic signal peptides did not disrupt the E. coli membrane vesicles. These results can be interpreted to indicate that the presequences of exported proteins interact specifically with a receptor either in the E. coli inner membrane or in the cytoplasmic fraction. However, biophysical data for the family of signal peptides studied here reveal that they will spontaneously insert into a lipid membrane at concentrations comparable to those that cause inhibition. Hence, an indirect effect mediated by the lipid bilayer of the membrane must be considered.

Conformations of signal peptides induced by lipids suggest initial steps in protein export

Despite the requirement for a functional signal sequence in protein export, little is known of the conformational properties and membrane interactions of these highly hydrophobic amino terminal extensions on nearly all exported proteins. The Escherichia coli lambda phage receptor signal sequence was studied in phospholipid monolayers by circular dichroism and Fourier transform infrared spectroscopy; the signal peptide was shown to prefer an alpha-helical conformation when inserted into the lipid phase. However, interaction with the lipid surface without insertion induced the signal sequence, which is unstructured in bulk aqueous solution, to adopt a beta structure. These observations are combined in a model for the initial steps in signal sequence-membrane interaction in vivo.

In vivo function and membrane binding properties are correlated for Escherichia coli lamB signal peptides

Wild-type and pseudorevertant signal peptides of the lamB gene product of Escherichia coli interact with lipid systems whereas a nonfunctional deletion mutant signal peptide does not. This conclusion is based on interaction of synthetic signal peptides with a lipid monolayer-water surface, conformational changes induced by presence of lipid vesicles in an aqueous solution of signal peptide, and capacities of the peptides to promote vesicle aggregation. Analysis of the signal sequences and previous conformational studies suggest that these lipid interaction properties may be attributable to the tendency of the functional signal peptides to adopt alpha-helical conformations. Although the possibility of direct interaction between the signal peptide and membrane lipids during protein secretion is controversial, the results suggest that conformationally related amphiphilicity and consequent membrane affinity of signal sequences are important for function in vivo.

Exploring the conformational roles of signal sequences: synthesis and conformational analysis of lambda receptor protein wild-type and mutant signal peptides

Secretion of the Escherichia coli lambda receptor protein (LamB protein) appears from genetic evidence to be correlated with the predicted tendency of its signal sequence to adopt an alpha-helical conformation [Emr, S. D., & Silhavy, T. J. (1983) Proc. Natl. Acad. Sci. U. S. A. 80, 4599]. We have tested this hypothesis by synthesizing major portions of signal sequences from the wild-type and mutant LamB proteins and analyzing their conformations by circular dichroism. The wild-type signal sequence contains a seven-residue hydrophobic region flanked by a proline and a glycine. Chou-Fasman rules predict that this segment will adopt an alpha-helical conformation. An export-deficient mutant is missing four residues from this region; the helix-breaking glycine and proline are thus separated by only three residues, and an alpha helix is not predicted to form. In each of the export-restored revertants, either the glycine or the proline is replaced with a residue which promotes helix formation. The helix content of the synthetic signal sequence fragments on the basis of CD measurements supports the secondary structure hypothesis described above. The relative helicity in aqueous sodium dodecyl sulfate, lysolecithin, or trifluoroethanol is as follows: wild type greater than R2 (Pro----Leu) greater than R1 (Gly----Cys) much greater than deletion mutant.

Fluorescence energy transfer studies on the active site of papain

Measurements have been performed of the excited-state lifetimes and fluorescence yields of papain tryptophan units when acyl derivatives of Phe-glycinal are bound at the active site of the enzyme. The enhancement of tryptophan fluorescence in complexes of papain with the acetyl or benzyloxycarbonyl derivatives is not stereospecific with respect to the configuration of the phenylalanyl residue, and the L and D isomers are equally effective as active-site-directed inhibitors of papain action. Evidence is offered in favor of the conclusion that this enhancement is primarily a consequence of the interaction of the phenylalanyl side chain of the inhibitor with Trp-69 of the enzyme. This residue can exchange fluorescence energy with the other four tryptophans of papain (Trp-7, Trp-26, Trp-177, Trp-181) upon excitation near their absorption maxima, but such "homotransfer" is absent if they are excited at the long-wave edge of their absorption spectra. Crystallographic data indicate that Trp-26 is most favorably positioned for efficient energy exchange with Trp-69, and the fluorescence data have been used to calculate a distance of 11 A between the two residues; this value is in satisfactory agreement with that found by crystallography. When derivatives of Phe-glycinal bearing an amino-terminal mansyl [6-(N-methylanilino)-2-naphthalene sulfonyl] group are bound at the active site of papain, the tryptophan fluorescence is quenched, as compared with that of the complex of papain with acetyl-Phe-glycinal, indicating energy transfer from papain tryptophan (most probably via Trp-26) to the fluorescent probe group. Although the L and D isomers of mansyl-Phe-glycinal are equally effective as inhibitors of papain action, the fluorescence quenching by the two isomers is different.

Phase transition in a lipid bilayer. II. Influence of adamantane derivatives

The influence of thirty-four adamantane, protoadamantane, and homoadamantane derivatives on the phase transition characteristics of the bilayer in dipalmitoyl lecithin liposomes has been determined by differential scanning calorimetry. Each of these compounds induces a broadening of the phase transition profile of the lipid bilayer that is dependent upon the concentration of the solute and its molecular structure. The concentration--response curves obtained for these solutes suggest that the cage compound derivatives modify the phase properties and under some conditions may induce a phase separation in the doped bilayer. The relative activity sequences obtained for the compounds examined cannot be accounted for by simple considerations of lipid/water partition coefficients, substitution constants based on free energy relationships, or the relative polarities or sizes of substituent groups. The observations are consistent with the hypothesis that the position and orientation of a solute within the bilayer are critical factors in determining its relative potency. The position of a solute within the bilayer is significantly controlled by the presence of polar substituents and by the relative geometric relationships of these groups. For a given substituent group, the shape and size of the hydrocarbon cage becomes increasingly important. It is apparent that seemingly minor modifications in the structure of a solute can significantly alter its influence on the phase transition behavior of a bilayer.