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Catalytic function of the conserved hydroxyl group in the protein tyrosine phosphatase signature motif.

Burst kinetics is observed with the Yersinia protein tyrosine phosphatase (PTPase). This provides direct kinetic evidence for a phosphoenzyme mechanism and suggests that the breakdown of the phosphoenzyme intermediate is the rate-limiting step. Burst kinetics is a powerful tool for mechanistic studies of PTPase catalysis since functional roles of active site residues can be evaluated by studying their effects on the individual elementary steps associated with the formation and the breakdown of the intermediate. In order to investigate the role of Thr410, a conserved residue that is present in the PTPase signature motif, this residue was altered by site-directed mutagenesis to serine and alanine. The effects of these mutations, as observed in both steady-state and pre-steady-state kinetic experiments with p-nitrophenyl phosphate (pNPP) as a substrate, demonstrated that the hydroxyl group of Thr410 is directly involved in catalysis. The hydroxyl group at residue 410 plays an important role in facilitating the breakdown of the phosphoenzyme intermediate.

Amino Acid Sequence↗

18O-exchange evidence that mutations of arginine in a signature sequence for P-type pumps affect inorganic phosphate binding.

We have proposed a model for part of the catalytic site of P-type pumps in which arginine in a signature sequence functions like lysine in P-loop-containing enzymes that catalyze adenosine 5'-triphosphate hydrolysis [Smirnova, I. N., Kasho, V. N., and Faller, L. D. (1998) FEBS Lett. 431, 309-314]. The model originated with evidence from site-directed mutagenesis that aspartic acid in the DPPR sequence of Na,K-ATPase binds Mg(2+) [Farley, R. A., et al. (1997) Biochemistry 36, 941-951]. It was developed by assuming that the catalytic domain of P-type pumps evolved from enzymes that catalyze phosphoryl group transfer. The functions of the positively charged amino group in P-loops are to bind substrate and to facilitate nucleophilic attack upon phosphorus by polarizing the gamma-phosphorus-oxygen bond. To test the prediction that the positively charged guanidinium group of R596 in human alpha(1) Na,K-ATPase participates in phosphoryl group transfer, the charge was progressively decreased by site-directed mutagenesis. Mutants R596K, -Q, -T, -M, -A, -G, and -E were expressed in yeast membranes, and their ability to catalyze phosphorylation with inorganic phosphate was evaluated by following (18)O exchange. R596K, in which the positive charge is retained, resembled the wild type. Substitution of a negative charge (R596E) resulted in complete loss of activity. The remaining mutants with uncharged side chains had both lowered affinity for inorganic phosphate and altered phosphate isotopomer distributions, consistent with increased phosphate-off rate constants compared to that of the wild type. Therefore, mutations of R596 strengthen our hypothesis that the oppositely charged side chains of the DPPR peptide in Na,K-ATPase form a quaternary complex with magnesium phosphate.

Amino Acid Sequence↗

Alanine-scanning mutagenesis in the signature disulfide loop of the glycine receptor alpha 1 subunit: critical residues for activation and modulation.

The glycine receptor enables the generation of inhibitory postsynaptic currents at synapses via neurotransmitter-dependent activation. These receptors belong to the ligand-gated ion channel gene superfamily, in which all members are comprised of five subunits, each of which possesses a signature 13-residue disulfide loop (Cys loop) in the extracellular domain. In this study, we used alanine-scanning mutagenesis of the residues between C138 and C152 of the Cys loop of the glycine receptor alpha1 subunit to identify residues critical for receptor activation and allosteric modulation. Mutation of L142, F145, or P146 to alanine produced decreases in the potency, maximal amplitude, and Hill coefficient for currents elicited by glycine and impaired receptor activation by the agonist taurine. These residues, along with D148, are positionally conserved in the family of LGIC subunits. Mutation at several other positions had little or no effect. The inhaled anesthetics halothane and isoflurane potentiate submaximal agonist responses at wild-type receptors, via an allosteric site. The mutations L142A, F145A, P146A, and D148A abolished positive modulation by these anesthetics, in some cases revealing a small inhibitory effect. A molecular model of the glycine receptor alpha1 subunit suggests that the Cys loop is positioned in a region of the receptor at the interface between the extracellular and transmembrane domains and that the critical functional residues identified here lie along the face of a predominantly hydrophobic surface. The present data implicate the Cys loop as an important functional moiety in the process of glycine receptor activation and allosteric regulation by anesthetics.

Alanine↗

Raman signature of the four-stranded intercalated cytosine motif in crystal and solution structures of DNA deoxycytidylates d(CCCT) and d(C8).

The Raman spectral signature of the four-stranded cytosine structure formed by intercalation of two hemiprotonated and parallel-stranded oligodeoxycytidylate duplexes (so-called i motif) has been obtained from the crystal structure of d(CCCT) [Kang, C.H., Berger, I., Lockshin, C., Ratliff, R., Moyzis, R., & Rich, A. (1994) Proc. Natl. Acad. Sci. U.S.A. 91, 11636-11640]. Identification of Raman markers diagnostic of the cytosine quadruplex is complemented by results obtained in a pH titration of 2'-deoxycytosine-5'-monophosphate (5'-dCMP) to show that the spectral fingerprint associated with N3 protonation of cytosine is distinct from that of quadruplex formation. The Raman spectrum thus provides a definitive basis for evaluating quantitatively both the extent of cytosine quadruplex formation and the degree of cytosine N3 protonation in DNA. Application to aqueous d(CCCT) and d(C8) demonstrates that the four-stranded intercalated structure is formed by both of these oligodeoxycytidylates in aqueous solution. Whereas both 5'-dCMP and the d(CCCT) quadruplex exhibit a midpoint of titration (apparent pKc) of 4.5 +/- 0.2 at 10 degrees C, cytosine protonation in d(C8) is shifted significantly toward the physiological range, with pKc = 5.8 +/- 0.2. The difference in pKc between the two quadruplexes is equivalent to a free energy difference of 1.7 kcal/mol at 10 degrees C. The present findings extend the library of Raman conformation markers to deoxycytidylate residues in the novel i quadruplex. The significance of these results for probing solution conformations of telomeric DNA sequences is also considered.

Base Sequence↗

Secret signatures inside genomic DNA.

A simple, practical method to watermark short trademarks or signatures into genomic DNA is introduced. Since the marking method is biologically innocuous, it can be applied to all commercialized bacteria to help establish brand names for the engineered strains and to resolve legal disputes regarding gene-related patents. The first such strain of Bacillus subtilis is engineered and is ready to be distributed.

Bacillus subtilis↗

The signature molecular descriptor. 4. Canonizing molecules using extended valence sequences.

We present a new algorithm to canonize molecular graphs using the signature molecular descriptor introduced in the previous papers of this series. While developed specifically for molecular structures, the algorithm can be used for any graph and is not limited to acyclic graphs, planar graphs, bounded valence, or bounded genus graphs, for which polynomial time algorithms exist. The algorithm is tested with benzenoid hydrocarbons and a database of 126,705 organic compounds. The algorithm's performances are compared against Brendan Mc Kay's Nauty algorithm, which is believed to be the fastest graph canonization algorithm for general graphs, with five series of graphs each comprising up to 30,000 vertices: 2D meshes (pericondensed benzenoids), 3D cages (fullerenes and nanotubes), 3D meshes (crystal lattices), 4D cages, and power law graphs (protein and gene networks). The algorithm can be downloaded as an open source code at http://www.cs.sandia.gov/ approximately jfaulon/QSAR.

Journal Article↗

Designing novel polymers with targeted properties using the signature molecular descriptor.

A method for solving the inverse quantitative structure-property relationship (QSPR) problem is presented which facilitates the design of novel polymers with targeted properties. Here, we demonstrate the efficacy of the approach using the targeted design of polymers exhibiting a desired glass transition temperature, heat capacity, and density. We present novel QSPRs based on the signature molecular descriptor capable of predicting glass transition temperature, heat capacity, density, molar volume, and cohesive energies of linear homopolymers with cross-validation squared correlation coefficients ranging between 0.81 and 0.95. Using these QSPRs, we show how the inverse problem can be solved to design poly(N-methyl hexamethylene sebacamide) despite the fact that the polymer was used not used in the training of this model.

Algorithms↗

Signature metabolites attesting to the in situ attenuation of alkylbenzenes in anaerobic environments.

Accurate assessment of the fate of hydrocarbons spilt in aquifers is essential for gauging associated health and ecological risks. Regulatory pressure to actively remediate such contaminated ecosystems can be substantially diminished if solid evidence for in situ microbial destruction of pollutants is obtained. In laboratory incubations, sediment-associated microorganisms from a gas condensate-contaminated aquifer anaerobically biodegraded toluene, ethylbenzene, xylene, and toluic acid isomers with stoichiometric amounts of sulfate consumed or methane produced. The activation of the alkylated aromatic contaminants involved conversion to their corresponding benzylsuccinic acid derivatives, a reaction known to occur for toluene and m-xylene decay, but one previously unrecognized for ethylbenzene, o- and p-xylene, and m-toluate metabolism. Benzylsuccinates were further biodegraded to toluates, phthalates, and benzoate. In laboratory incubations, these metabolites were transiently produced. Several of the metabolites were also detected in groundwater samples from an aquifer where alkylbenzene concentrations decreased over time, suggesting that anaerobic microbial metabolism of these contaminants also occurs in situ. Our studies confirm the utility of the aforementioned compounds as signature metabolites attesting to the natural attenuation of aromatic hydrocarbons in anaerobic environments.

Bacteria, Anaerobic↗

Carbon isotope signature of polycyclic aromatic hydrocarbons (PAHs): evidence for different sources in tropical and temperate environments?

In tropical soils, naphthalene and, partly also, perylene occur at elevated concentrations while pyrolytic higher molecular weight PAHs are almost absent. We hypothesize that there are recent biological PAH sources in the tropical environment related with woody plants and termites. We used the C isotope signature of individual PAHs in temperate and tropical soils and in tropical wood and termite nests to distinguish different PAH sources. The mean delta13C values of the benzo[b+j+k]fluoranthenes and of benzo[a+e]pyrenes in temperate soils ranged between -24.6/1000 and -25.3/1000, being similar to values reported in the literature for PAHs with pyrolitic origin. The mean delta13C values of perylene decreased in the order temperate soils (-27.0/1000) > termite nests (-31.4/1000) > tropical soil (-32.4/1000), while those of naphthalene (-24.6/1000 to -26.2/1000) were similar among the tropical and temperate soils, tropical wood, and termite nests. Our results support the assumption that perylene in the tropical environment is recently biologically produced, as indicated by the depletion in 13C. The C isotope composition of naphthalene, however, cannot be used to distinguish different sources.

Animals↗

Geochemical signature of contaminated sediment remobilization revealed by spatially resolved X-ray microanalysis of annual rings of Salix nigra.

An X-ray microprobe was used to determine the concentration and distribution of Ni, U, and other metals within annual rings of willows (Salix nigra L.) from a former de facto radiological settling basin (Steed Pond; SP) and a depositional environment downstream (Tims Branch; TB) on the Savannah River Site (SRS). Geochemical and historical information about both areas are well documented. Following spillway breaches at SP in 1984 and the early 1990s, TB is inundated with contaminated sediments during storms. Bulk elemental composition of tree cores was determined using ICP-OES. Synchrotron X-rayfluorescence (SXRF) analysis showed that the metal contents of SP and TB cores were an order of magnitude higher than those from a reference site. TB cores were enriched with Ni in 1984 and 1991, corresponding with SP spillway breaches (containing 790 mg kg(-1) Ni in 1991). Cores from SP exhibited an extremely high Ni peak in 1996, approximately 5000 mg kg(-1), even though contaminant levels at SP did not change. The geochemical signature of contaminants recorded in TB annual rings reflected the significant sediment remobilization events consistent with the detailed history of the site, and at concentrations relative to their proximity to the source term. However, physiological processes occurring within impacted trees strongly influence the chronological accuracy of dendroanalysis and must be investigated further.

Environmental Monitoring↗

Isotopic signature and impact of car catalysts on the anthropogenic osmium budget.

Higher osmium concentrations and lower 187Os/188Os ratios in sediments from urban areas have been linked to anthropogenic osmium sources. Automobile catalytic converters that use platinum group metals (PGM) are a potential source for this Os pollution. We present the first direct Os concentrations and isotopic measurements of catalytic converters for major automobile brands to test the assumption that car catalysts release Os with a distinct signature in the environment. The analysis of four new catalytic converters yields similar low 187Os/188Os ratios (0.1-0.2), suggesting a similar source for the PGM. The Os concentrations measured are in the ppt range (6-228 ppt). From our results, the osmium contribution of the car catalysts to the environment through attrition (wearing and grinding down of the catalyst by friction) is predicted to be low, <0.2 pg Os/m2/year in highly urbanized environment. We show that Os loss from catalysts as volatile OsO4 is important at car catalyst operating temperatures. Moreover, we estimate that car catalysts may be responsible for up to approximately 120 pg Os/m2 deposited per year in urban areas and that part of it may be exported to sedimentary sinks. Car catalytic converters are thus an important anthropogenic osmium source in densely populated areas. The NIST car catalyst standard (SRM-2557, made from recycled used catalysts) yields higher concentrations (up to 721 ppt Os) and a more radiogenic isotopic composition (approximately 0.38), perhaps indicative of Os contamination during its preparation.

Automobiles↗

Signatures of beta-peptide unfolding in two-dimensional vibrational echo spectroscopy: a simulation study.

An ensemble of exciton Hamiltonians for the amide-I band of the folded and unfolded states of a helical beta-heptapeptide is generated using a molecular dynamics (MD) simulation. The correlated fluctuations of its parameters and their signatures in two-dimensional (2D) vibrational echo spectroscopy are computed. This technique uses infrared pulse sequences to provide ultrafast snapshots of molecular structural fluctuations, in analogy with multidimensional NMR. The present study demonstrates that, by combining a method of calculating the vibrational Hamiltonian from MD snapshots and the nonlinear exciton equations (NEE), it may be possible to simulate realistic multidimensional IR spectra of chemically and biologically interesting systems.

Computer Simulation↗

Dual species emission from single polyfluorene molecules: signatures of stress-induced planarization of single polymer chains.

Single chains of the conjugated polymer polyfluorene are shown to exist in two distinct conformational arrangements. Planarization of the chain to the single molecule beta-phase leads to a red shift in the emission and a strong modification of the vibronic progression. Most importantly, this structural rearrangement dramatically affects the photophysical stability on the single molecule level. Single molecule beta-phase emission displays a vastly improved lifetime and much less noise on both the emission intensity and the spectral position. In the absence of signatures of multichromophoric emission on the single molecule level, we propose that the effective conjugation length accounts for most of the physical chain length of the beta-phase.

Journal Article↗

A new approach to the characterization of volatile signatures of cork wine stoppers.

This work describes a new method for the rapid characterization of volatile compounds of cork wine stoppers by a dynamic headspace method coupled to mass spectrometry (DHS-MS). This technique does not require any pretreatment of the sample. The global volatile signature of the cork is evaluated without real chromatographic separation of its constituents. For data analysis, the mass fragments of each spectrum (50 < m/z <180 amu) were considered as potential descriptors of the composition of the cork sample headspace. Chemometrics methods (principal component analysis and partial least-squares regression) were applied to extract useful information by selecting the most significant mass fragments (m/z) that allowed a good classification of the cork samples studied. In the present work, geographical origin of cork samples could be successfully characterized and predicted.

Food Packaging↗

Signature of nanodiamond in Raman spectra: a density functional theoretical study.

Nanocrystalline diamond (NCD) has attracted great attention both experimentally and theoretically in the past few years. The identification of the presence and the amount of NCD in amorphous carbon film has been a challenging issue. Although Raman spectroscopy has become a standard tool for the characterization of various carbon phases, a simple criterion for identifying NCD has not yet been well-established. In the present work, a theoretical study of the Raman spectra of the model compounds of NCD is presented on the basis of the density functional calculations. The reliability of the computational approach has been tested by comparing the predicated Raman spectra of several reference molecules to those obtained experimentally. To show the unique Raman spectrum of a NCD phase, a series of the model compounds of various carbon materials including tetrahedral and hexagonal clusters, and trans-polyacetylene fragments, were considered, and subsequently their Raman spectra below 2000 cm(-1) were calculated and compared with each other. The calculated results indicate that the relatively stronger broad peak at about 480 cm(-1) could be used as the signature of a NCD phase in the sample.

Journal Article↗

Stability and signatures of biexcitons in carbon nanotubes.

The linear optical properties of semiconducting carbon nanotubes are dominated by quasi-one-dimensional excitons formed by single electron-hole pairs. Hence, the nonlinear response at high pump levels most likely leads to the formation of exciton complexes involving several electron-hole pairs. Such complexes would therefore play an important role in, e.g., lasing applications. We demonstrate here that the biexciton complex is surprisingly stable for nanotubes in a wide diameter range. Theoretical predictions for the signature of such states in pump-probe spectroscopy are presented.

Computer Simulation↗

Composite organic-inorganic nanoparticles (COINs) with chemically encoded optical signatures.

To obtain a coding system for multiplex detection, we have developed a method to synthesize a new type of nanomaterial called composite organic-inorganic nanoparticles (COINs). The method allows the incorporation of a broad range of organic compounds into COINs to produce surface enhanced Raman scattering (SERS)-like spectra that are richer in variety than fluorescence-based signatures. Preliminary data suggest that COINs can be used as Raman tags for multiplex and ultrasensitive detection of biomolecules.

Gold↗

Signatures of molecular magnetism in single-molecule transport spectroscopy.

We report single-molecule-transistor measurements on devices incorporating magnetic molecules. By studying the electron-tunneling spectrum as a function of magnetic field, we are able to identify signatures of magnetic states and their associated magnetic anisotropy. A comparison of the data to simulations also suggests that sequential electron tunneling may enhance the magnetic relaxation of the magnetic molecule.

Computer Simulation↗