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PubMed1984

A fast method of comparing protein structures.

Comparative studies on protein structures form an integral part of protein crystallography. Here, a fast method of comparing protein structures is presented. Protein structures are represented as a set of secondary structural elements. The method also provides information regarding preferred packing arrangements and evolutionary dynamics of secondary structural elements. This information is not easily obtained from previous methods. In contrast to those methods, the present one can be used only for proteins with some secondary structure. The method is illustrated with globin folds, cytochromes and dehydrogenases as examples.

Animals↗

PubMed1988

Isolation of the tachykinin, des[Ser1Pro2]scyliorhinin II from the intestine of the ray, Torpedo marmorata.

A peptide with neurokinin A-like immunoreactivity was isolated from an extract of the intestine of an elasmobranch fish, Torpedo marmorata. The primary structure of the peptide was established as Ser-Asn-Ser-Lys-Cys-Pro-Asp-Gly-Pro-Asp-Cys-Phe-Val-Gly-Leu-Met.NH2. This amino acid sequence is identical to that of residues (3-18) of scyliorhinin II previously isolated from the intestine of the common dogfish (Scyliorhinus canicula). The presence of the truncated peptide, lacking Ser-Pro, in the Torpedo gut suggests that scyliorhinin II may be a substrate for an enzyme with dipeptidylpeptidase IV-like specificity. The data support previous assertions that strong evolutionary pressure has acted within the elasmobranch subclass of chondrichthyean fish to conserve the structures of regulatory peptides.

Amino Acids↗

PubMed1986

Amino acids of the Murchison meteorite. III. Seven carbon acyclic primary alpha-amino alkanoic acids.

All of the eighteen possible seven-carbon acyclic primary alpha-amino alkanoic acids have been positively identified in a hot-water extract of the Murchison meteorite by the combined use of gas chromatography-mass spectrometry, ion exchange chromatography and reversed-phase chromatography. None of these amino acids has previously been found in meteorites or in any other natural material. They range in concentration from < or = 0.5 to 5.3 nmol g-1. Configuration assignments were made for 2-amino-3,4-dimethylpentanoic acid and allo-2-amino-3,4-dimethylpenatonoic acid and the diasteromer ratio was determined. Fifty-five amino acids have now been positively identified in the Murchison meteorite, 36 of which are unknown in terrestrial materials. This unique suite of amino acids is characterized by the occurrence of all structural isomers within the two major classes of amino acids represented, by the predominance of branched chain isomers, and by an exponential decline in amount with increasing carbon chain length within homologous series. These characteristics of the Murchison amino acids are suggestive of synthesis before incorporation into a parent body.

Amino Acids↗

PubMed1987

The role of minerals in the thermal alteration of organic matter--IV. Generation of n-alkanes, acyclic isoprenoids, and alkenes in laboratory experiments.

A series of pyrolysis experiments, utilizing two different immature oil-prone kerogens ("type I": Green River Formation kerogen; "Type II": Monterey Formation kerogen) mixed with common sedimentary minerals (calcite, illite, or Na-montmorillonite), was conducted to study the effects of minerals on the generation of n-alkanes, acyclic isoprenoids, and alkenes during laboratory-simulated catagenesis of kerogen. The influence of clay minerals on the aliphatic hydrocarbons is critically dependent on the water concentration during laboratory thermal maturation. Under extremely low contents of water (i.e., dry pyrolysis, where only pyrolysate water is present), C12(+) -range n-alkanes and acyclic isoprenoids are mostly destroyed by montmorillonite but undergo only minor alteration with illite. Both clay minerals significantly reduce alkene formation during dry pyrolysis. Under hydrous conditions (mineral/water = 2:1), the effects of the clay minerals are substantially reduced. In addition, the dry pyrolysis experiments show that illite and montmorillonite preferentially retain large amounts of the polar constituents of bitumen, but not n-alkanes or acyclic isoprenoids. Therefore, bitumen fractionation according to polarity differences occurs in the presence of these clay minerals. By this process, n-alkanes and acyclic isoprenoids are concentrated in the bitumen fraction that is not strongly adsorbed on the clay matrices. The extent of these concentrations effects is greatly diminished during hydrous pyrolysis. In contrast, calcite has no significant influence on the thermal evolution of the hydrocarbons. In addition, calcite is incapable of retaining bitumen. Therefore, the fractionation of n-alkanes or acyclic isoprenoids relative to the polar constituents of bitumen is insignificant in the presence of calcite.

Alkanes↗

PubMed1992

Organic compounds in the Forest Vale, H4 ordinary chondrite.

We have analyzed the H4 ordinary chondrite Forest Vale for polycyclic aromatic hydrocarbons (PAHs) using two-step laser mass spectrometry (L2MS) and for amino acids using a standard chromatographic method. Indigenous PAHs were identified in the matrices of freshly cleaved interior faces but could not be detected in pulverized silicates and chondrules. No depth dependence of the PAHs was found in a chipped interior piece. Amino acids, taken from the entire sample, consisted of protein amino acids that were nonracemic, indicating that they are terrestrial contaminants. The presence of indigenous PAHs and absence of indigenous amino acids provides support for the contention that different processes and environments contributed to the synthesis of the organic matter in the solar system.

Amino Acids↗

PubMed1995

Thermal synthesis of amino acids and the origin of life.

The recent review by Marshall (1994) of the production of amino acids from the interstellar components, formaldehyde and ammonia, is placed in the larger context of the origin of life. Thermal energy, being ubiquitous in the Earth, emerges as the sole necessary form of energy. To appreciate the overview of the natural evolutionary sequence it is necessary to recognize stepwiseness in evolution, a principle that has however been often ignored. Since self organization of thermal protein to cells is instantaneous, but only one step in a geochemical ladder, individual steps may be regarded as instantaneous, while the sequence requires measurable time. Two steps indicated are extrusion of a hot, dry organic magma of amino acids --> peptides into an aqueous environment in which occurs a second step of self organization. In this paper, spinoffs of the defensible theory for the origin of life have been briefly reviewed as a fundamental consequence of nonrandom thermal copolymerization of amino acids.

Amino Acids↗

PubMed1996

A reexamination of amino acids in lunar soils: implications for the survival of exogenous organic material during impact delivery.

Using a sensitive high performance liquid chromatography technique, we have analyzed both the hot water extract and the acid hydrolyzed hot water extract of lunar soil collected during the Apollo 17 mission. Both free amino acids and those derived from acid labile precursors are present at a level of roughly 15 ppb. Based on the D/L amino acid ratios, the free alanine and aspartic acid observed in the hot water extract can be entirely attributed to terrestrial biogenic contamination. However, in the acid labile fraction, precursors which yield amino acids are apparently present in the lunar soil. The amino acid distribution suggests that the precursor is probably solar wind implanted HCN. We have evaluated our results with regard to the meteoritic input of intact organic compounds to the moon based on an upper limit of < or = 0.3 ppb for alpha-aminoisobutyric acid, a non-protein amino acid which does not generally occur in terrestrial organisms and which is not a major amino acid produced from HCN, but which is a predominant amino acid in many carbonaceous chondrites. We find that the survival of exogenous organic compounds during lunar impact is < or = 0.8%. This result represents an example of minimum organic impact survivability. This is an important first step toward a better understanding of similar processes on Earth and on Mars, and their possible contribution to the budget of prebiotic organic compounds on the primitive Earth.

Amino Acids↗

PubMed1996

Small SiC grains and a nitride grain of circumstellar origin from the Murchison meteorite: implications for stellar evolution and nucleosynthesis.

We report the results of SIMS isotopic analyses of carbon, nitrogen, oxygen, and silicon made on 849 small (approximately 1 micrometer) individual silicon carbide grains from the Murchison meteorite. The isotopic compositions of the major elements carbon and silicon of most grains (mainstream) are similar to those observed in larger grain studies suggesting an AGB star origin of these grains. In contrast, the trace element nitrogen shows a clear dependency on grain size. 14N/15N ratios increase with decreasing grain size, suggesting different stellar sources for grains of different size. Typically observed 14N/15N ratios in the small grains of this study are approximately 2700, clearly larger than the values expected from model calculations of AGB stars. In addition to the three dredge-up episodes characteristic for the evolution of AGB stars, extra-mixing of CNO-processed matter in low mass AGB stars appears to be a promising possibility in order to explain the high 14N/15N ratios of the small circumstellar SiC grains. A small fraction of grains shows a silicon isotopic signature not observed in larger circumstellar SiC grains from Murchison. Their stellar origin is still uncertain. The minor type A, B, Y, and X grains were found to be present at a level of a percent, which is similar to their abundance in the larger-grain SiC separates from Murchison. Oxygen isotopic compositions are normal within the experimental uncertainties of several 10%, indicating that oxygen of stellar origin is rare or even absent in the SiC grains. We conclude that most of the oxygen is a contaminant which was introduced into the SiC grains after their formation, e.g., during sample processing in the laboratory. We identified a nitride grain, most likely Si3N4 with little carbon, with highly anomalous isotopic compositions (12C/13C = 157 +/- 33, 14N/15N = 18 +/- 1, delta 29 Si = -43 +/- 56%, delta 30 Si = -271 +/- 50%). The isotopic patterns of carbon, nitrogen, and silicon resemble those of the rare SiC X grains suggesting that these two rare constituents of circumstellar matter formed in the same type of stellar source, namely, Type II supernovae.

Carbon↗

PubMed1986

Amino acids derived from Titan tholins.

An organic heteropolymer (Titan tholin) was produced by continuous dc discharge through a 0.9 N2/0.1 CH4 gas mixture at 0.2 mbar pressure, roughly simulating the cloudtop atmosphere of Titan. Treatment of this tholin with 6N HCl yielded 16 amino acids by gas chromatography after derivatization of N-trifluroacetyl isopropyl esters on two different capillary columns. Identifications were confirmed by GC/MS. Glycine, aspartic acid, and alpha- and beta-alanine were produced in greatest abundance; the total yield of amino acids was approximately 10(-2), approximately equal to the yield of urea. The presence of "nonbiological" amino acids, the absence of serine, and the fact that the amino acids are racemic within experimental error together indicate that these molecules are not due to microbial or other contamination, but are derived from the tholin. In addition to the HCN, HC2CN, and (CN)2 found by Voyager, nitriles and aminonitriles should be sought in the Titanian atmosphere and, eventually, amino acids on the surface. These results suggest that episodes of liquid water in the past or future of Titan might lead to major further steps in prebiological organic chemistry on that body.

Amino Acids↗

PubMed1966