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Does Chirality Influence the Stability of Amino Acid –Cu Complexes in the Salt-Induced Peptide Formation Reaction? Insights from Density Functional Theory Calculations

The polymerization of amino acids into peptides and ultimately proteins is critical to evolution of life. Ribosomally-synthesized proteins are homochiral, composed entirely of L-amino acids. Abiotic syntheses of amino acids, however, produce racemic mixtures(equal amounts of L and D enantiomers), meaning that the pool of monomers available for abiotic protein synthesis would be racemic or nearly so. There are no prebiotically plausible mechanisms known to yield homochiral peptides from racemic pools of amino acids. While some mechanisms capable of producing or amplifying enantiomeric excesses have been observed, these excesses are small or not applicable to all biologically relevant amino acids. As a result, a prebiotically-feasible mechanism to create enantiopure pools of amino acids has not been identified. However, it is not clear that these enantio-enriched or enantiopure pools are necessary to produce homochiral peptides. Steric and electronic effects, or a combination of both, may influence how different enantiomers interact with each other, potentially leading to homochiral peptides from racemic mixtures. Here, we use density functional theory (DFT) calculations to assess the stability of homochiral and heterochiral reactive complexes produced during polymerization via the salt-induced peptide formation (SIPF) reaction. Experimental studies of the SIPF reaction have shown that it enables the formation of peptides under diverse environmental conditions, making it a plausible pathway to peptide formation on early Earth. In the SIPF reaction, NaCl acts as a condensation reagent while a divalent metal cation, primarily Cu2+, facilitates polymerization by complexing and activating amino acids forming a monochlorocuprate complex. To assess if hetero-or homochiral monochlorocuprate complexes were energetically favored, we compared the stability of LL, DD, and LD enantiomers of Cu2+–(alanine)2and Cu2+–(valine) 2 complexes. Gaussian 09 density DFT energy-minimization calculations were made for each Cu –amino acid complex in the cis and trans configuration. Models were energy minimized using the BH and HLYP/6-31++G(d,p) level of theory and free energies were compared to determine the most stable configuration.

A C Fox↗
NASA NTRS2012

Unusual Nonterrestrial L-proteinogenic Amino Acid excesses in the Tagish Lake Meteorite

The distribution and isotopic and enantiomeric compositions of amino acids found in three distinct fragments of the Tagish Lake C2-type carbonaceous chondrite were investigated via liquid chromatography with fluorescence detection and time-of-flight mass spectrometry and gas chromatography isotope ratio mass spectrometry. Large L-enantiomeric excesses (L(sub ee) approximately 43-59%) of the alpha-hydrogen aspartic and glutamic amino acids were measured in Tagish Lake, whereas alanine, another alpha hydrogen protein amino acid, was found to be nearly racemic (D much approximately L) using both techniques. Carbon isotope measurements of D- and L-aspartic acid and 1)- and L-alanine in Tagish Lake fall well outside of the terrestrial range and indicate that the measured aspartic acid enantioenrichment is indigenous to the meteorite. Alternate explanations for the L-excesses of aspartic acid such as interference from other compounds present in the sample, analytical biases, or terrestrial amino acid contamination were investigated and rejected. These results can be explained by differences in the solid-solution phase behavior of aspartic acid, which can form conglomerate enantiopure solids during crystallization, and alanine, which can only form racemic crystals. Amplification of a small initial L-enantiomer excess during aqueous alteration on the meteorite parent body could have led to the large L-enrichments observed for aspartic acid and other conglomerate amino acids in Tagish Lake. The detection of non terrestrial L-proteinogenic amino acid excesses in the Tagish Lake meteorite provides support for the hypothesis that significant enantiomeric enrichments for some amino acids could form by abiotic processes prior to the emergence of life.

Glavin, Daniel P.↗
NASA NTRS2006

Bacterial Utilization of L-sugars and D-amino Acids

The fact that organotrophic organisms on Earth use L-amino acids and D-sugars as an energy source is recognized as one of the universal features of life. The chirality of organic molecules with asymmetric location of group- radicals was described a relatively long time ago. In 1848, Louis Pasteur discovered chiral molecules when he investigated the way that crystals of sodium ammonium paratartrate rotated the plane of polarization of light. He found that the crystal structures represented the underlying asymmetry of molecules that existed in either lea-handed or right-handed forms (enantiomers). Pasteur observed that abiotic (chemical) processes produced mixtures with equal numbers (racemic) of the two forms but that living organisms possessed a molecular asymmetry that included only one of the enantiomers (homochirality). He speculated that the origin of the asymmetry of chiral biomolecules might hold the key to the nature of life. All of the amino acids in proteins (except for Glycine which is symmetrical) exhibit the same absolute steric configuration as L-glyceraldehyde. D-amino acids are never found in proteins, although they do exist in nature and are often found in polypeptide antibiotics. Constitutional sugars of cells, opposite to the amino acids, are the D-enantiomers, and the appearance of L-sugars in Nature is extremely rare. Notwithstanding this fact, the metabolism of some bacteria does have capability to use amino acids and sugars with alternative chirality. This property may be caused by the function of specific enzymes belonging to the class of isomerases (racemases, epimerases, isomerases, tautomerases). In our laboratory, we have investigated several anaerobic bacterial strains, and have found that some of these bacteria are capable of using D-amino acids and L-sugars. Strain BK1 is capable of growth on D-arginine, but its growth characteristics on L-arginine are approximately twice higher. Another alkaliphilic strain SCAT(sup T) (= ATCC BAA-1084(sup T)= JCM 12857(sup T) = DSM 17722(sup T) = CIP 107910(sup T)) was found to be capable of growth on L-ribose and L-arabinose. It is interesting that this strain was incapable of growth on D-arabinose, which suggests the involvement of some alternative mechanism of enzyme activity. In this paper, we describe the preliminary results of these microbiological studies and discuss some possible implications.

Pikuta, Elena↗
NASA NTRS2022

A Closer Look at Non-Random Patterns Within Chemistry Space for a Smaller, Earlier Amino Acid Alphabet

Recent findings, in vitro and in silico, are strengthening the idea of a simpler, earlier stage of genetically encoded proteins which used amino acids produced by prebiotic chemistry. These findings motivate a re-examination of prior work which has identified unusual properties of the set of twenty amino acids found within the full genetic code, while leaving it unclear whether similar patterns also characterize the subset of prebiotically plausible amino acids. We have suggested previously that this ambiguity may result from the low number of amino acids recognized by the definition of prebiotic plausibility used for the analysis. Here, we test this hypothesis using significantly updated data for organic material detected within meteorites, which contain several coded and non-coded amino acids absent from prior studies. In addition to confirming the well-established idea that “late” arriving amino acids expanded the chemistry space encoded by genetic material, we find that a prebiotically plausible subset of coded amino acids generally emulates the patterns found in the full set of 20, namely an exceptionally broad and even distribution of volumes and an exceptionally even distribution of hydrophobicities (quantified as logP) over a narrow range. However, the strength of this pattern varies depending on both the size and composition the library used to create a background (null model) for a random alphabet, and the precise definition of exactly which amino acids were present in a simpler, earlier code. Findings support the idea that a small sample size of amino acids caused previous ambiguous results, and further improvements in meteorite analysis, and/or prebiotic simulations will further clarify the nature and extent of unusual properties. We discuss the case of sulfur-containing amino acids as a specific and clear example and conclude by reviewing the potential impact of better understanding the chemical “logic” of a smaller forerunner to the standard amino acid alphabet.

Amino acids↗
NASA NTRS2008

Nanoflow Separation of Amino Acids for the Analysis of Cosmic Dust

The delivery of amino acids to the early Earth by interplanetary dust particles, comets, and carbonaceous meteorites could have been a significant source of the early Earth's prebiotic organic inventory. Amino acids are central to modern terrestrial biochemistry as major components of proteins and enzymes and were probably vital in the origin of life. A variety of amino acids have been detected in the CM carbonaceous meteorite Murchison, many of which are exceptionally rare in the terrestrial biosphere including a-aminoisobutyric acid (AIB) and isovaline. AIB has also been detected in a small percentage of Antarctic micrometeorite grains believed to be related to the CM meteorites We report on progress in optimizing a nanoflow liquid chromatography separation system with dual detection via laser-induced-fluorescence time of flight mass spectrometry (nLC-LIF/ToF-MS) for the analysis of o-phthaldialdehydelN-acetyl-L-cysteine (OPA/NAC) labeled amino acids in cosmic dust grains. The very low flow rates (<3 micro-L/min) of nLC over analytical LC (>0.1 ml/min) combined with <2 micron column bead sizes has the potential to produce efficient analyte ionizations andchromatograms with very sharp peaks; both increase sensitivity. The combination of the selectivity (only primary amines are derivatized), sensitivity (>4 orders of magnitude lower than traditional GC-MS techniques), and specificity (compounds identities are determined by both retention time and exact mass) makes this a compelling technique. However, the development of an analytical method to achieve separation of compounds as structurally similar as amino acid monomers and produce the sharp peaks required for maximum sensitivity is challenging.

Martin, M. P.↗
NASA NTRS1977

Light-Activated Amino Acid Transport Systems in Halobacterium halobium Envelope Vesicles: Role of Chemical and Electrical Gradients

The accumulation of 20 commonly occurring L-amino acids by cell envelope vesicles of Halobacterium halobium, in response to light-induced membrane potential and an artificially created sodium gradient, has been studied. Nineteen of these amino acids are actively accumulated under either or both of these conditions. Glutamate is unique in that its uptake is driven only by a chemical gradient for sodium. Amino acid concentrations at half-maximal uptake rates (Km) and maximal transport rates (V(sub max) have been determined for the uptake of all 19 amino acids. The transport systems have been partially characterized with respect to groups of amino acids transported by common carriers, cation effects, and relative response to the electrical and chemical components of the sodium gradient, the driving forces for uptake. The data presented clearly show that the carrier systems, which are responsible for uptake of individual amino acids, are as variable in their properties as those found in other organisms, i. e., some are highly specific for individual amino acids, some transport several amino acids competitively, some are activated by a chemical gradient of sodium only, and some function also in the complete absence of such a gradient. For all amino acids, Na(+) and K(+) are both required for maximal rate of uptake. The carriers for L-leucine and L-histidine are symmetrical in that these amino acids are transported in both directions across the vesicle membrane. It is suggested that coupling of substrate transport to metabolic energy via transient ionic gradients may be a general phenomenon in procaryotes.

MacDonald, Russell E.↗
NASA NTRS1973

Accumulated analyses of amino acid precursors in returned lunar samples

Six amino acids (glycine, alanine, aspartic acid, glutamic acid, serine, and threonine) obtained by hydrolysis of extracts have been quantitatively determined in ten collections of fines from five Apollo missions. Although the amounts found, 7-45 ng/g, are small, the lunar amino acid/carbon ratios are comparable to those of the carbonaceous chondrites, Murchison and Murray, as analyzed by the same procedures. Since both the ratios of amino acid to carbon, and the four or five most common types of proteinous amino acid found, are comparable for the two extraterrestrial sources despite different cosmophysical histories of the moon and meteorites, common cosmochemical processes are suggested.

Fox, S. W.↗
NASA NTRS1989

The search for and identification of amino acids, nucleobases and nucleosides in samples returned from Mars

An investigation of the returned Mars samples for biologically important organic compounds, with emphasis on amino acid, the puring and pyrimidine bases, and nucleosides is proposed. These studies would be conducted on subsurface samples obtained by drilling past the surface oxidizing layer with emphasis on samples containing the larges quantities of organic carbon as determined by the rover gas chromatographic mass spectrometer (GCMS). Extraction of these molecules from the returned samples will be performed using the hydrothermal extraction technique described by Cheng and Ponnamperuma. More rigorous extraction methods will be developed and evaluated. For analysis of the extract for free amino acids or amino acids present in a bound or peptidic form, aliquots will be analyzed by capillary GCMS both before and after hydrolysis with 6N hydrochloric acid. Establishment of the presence of amino acids would then lead to the next logical step which would be the use of chiral stationary gas chromatography phases to determine the enatiomeic composition of the amino acids present, and thus potentially establish their biotic or abiotic origin. Confirmational analyses for amino acids would include ion-exchange and reversed-phase liquid chromatographic analysis. For analyses of the returned Mars samples for nucleobases and nucleosides, affinity and reversed-phase liquid chromatography would be utilized. This technology coupled with scanning UV detection for identification, presents a powerful tool for nucleobase and nucleoside analysis. Mass spectrometric analysis of these compounds would confirm their presence in samples returned form Mars.

Gehrke, Charles W.↗
NASA NTRS1996

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 less than or equal to 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 less than or equal to 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.

Brinton, Karen L. F.↗
NASA NTRS1972

Evolution from amino acids - Lunar occurrence of their precursors.

Review of the present state of experimentally based concepts of organic evolution from amino acids. Earlier studies of the synthesis of amino acid precursors from meteoritic material, lunar dust, and terrestrial lava are briefly summarized, and laboratory experiments in which polymers of amino acids were obtained either by direct heating of dry amino acids or by heating aqueous solutions of mixtures of amino acids are described. In particular, a process is described by which alpha-amino acids were made to react to form linear chains of proteinoids. It is concluded that a proteinoid microsystem was a common ancestor of all life on earth.

Fox, S. W.↗
NASA NTRS1994

Amino acid racemization in amber-entombed insects: implications for DNA preservation

DNA depurination and amino acid racemization take place at similar rates in aqueous solution at neutral pH. This relationship suggests that amino acid racemization may be useful in accessing the extent of DNA chain breakage in ancient biological remains. To test this suggestion, we have investigated the amino acids in insects entombed in fossilized tree resins ranging in age from <100 years to 130 million years. The amino acids present in 40 to 130 million year old amber-entombed insects resemble those in a modern fly and are probably the most ancient, unaltered amino acids found so far on Earth. In comparison to other geochemical environments on the surface of the Earth, the amino acid racemization rate in amber insect inclusions is retarded by a factor of >10(4). These results suggest that in amber insect inclusions DNA depurination rates would also likely be retarded in comparison to aqueous solution measurements, and thus DNA fragments containing many hundreds of base pairs should be preserved. This conclusion is consistent with the reported successful retrieval of DNA sequences from amber-entombed organisms.

NASA Discipline Exobiology↗
NASA NTRS2011

Heterogeneous Distributions of Amino Acids Provide Evidence of Multiple Sources Within the Almahata Sitta Parent Body, Asteroid 2008 TC(sub 3)

Two new fragments of the Almahata Sitta meteorite and a sample of sand from the related strewn field in the Nubian Desert, Sudan, were analyzed for two to six carbon aliphatic primary amino acids by ultrahigh performance liquid chromatography with UV-fluorescence detection and time-of-flight mass spectrometry (LC-FT/ToF-MS). The distribution of amino acids in fragment #25, an H5 ordinary chondrite, and fragment #27, a polymict ureilite, were compared with results from the previously analyzed fragment #4, also a polymict ureilite. All three meteorite fragments contain 180-270 parts-per-billion (ppb) of amino acids, roughly 1000-fold lower than the total amino acid abundance of the Murchison carbonaceous chondrite. All of the Almahata Sitta fragments analyzed have amino acid distributions that differ from the Nubian Desert sand, which primarily contains L-alpha-amino acids. In addition, the meteorites contain several amino acids that were not detected in the sand, indicating that many of the amino acids are extraterrestrial in origin. Despite their petrological differences, meteorite fragments #25 and #27 contain similar amino acid compositions; however, the distribution of amino acids in fragment #27 was distinct from those in fragment #4, even though both arc polymict ureilites from the same parent body. Unlike in CM2 and CR2/3 meteorites, there are low relative abundances of alpha-amino acids in the Almahata Sitta meteorite fragments, which suggest that Strecker-type chemistry was not a significant amino acid formation mechanism. Given the high temperatures that asteroid 2008 TC3 appears to have experienced and lack of evidence for aqueous alteration on the asteroid, it is possible that the extraterrestrial amino acids detected in Almahata Sitta were formed by Fischer-Tropsch/Haber-Bosch type gas-grain reactions at elevated temperatures.

Burton, Aaron S.↗
NASA NTRS1992

Suppression of muscle protein turnover and amino acid degradation by dietary protein deficiency

To define the adaptations that conserve amino acids and muscle protein when dietary protein intake is inadequate, rats (60-70 g final wt) were fed a normal or protein-deficient (PD) diet (18 or 1% lactalbumin), and their muscles were studied in vitro. After 7 days on the PD diet, both protein degradation and synthesis fell 30-40% in skeletal muscles and atria. This fall in proteolysis did not result from reduced amino acid supply to the muscle and preceded any clear decrease in plasma amino acids. Oxidation of branched-chain amino acids, glutamine and alanine synthesis, and uptake of alpha-aminoisobutyrate also fell by 30-50% in muscles and adipose tissue of PD rats. After 1 day on the PD diet, muscle protein synthesis and amino acid uptake decreased by 25-40%, and after 3 days proteolysis and leucine oxidation fell 30-45%. Upon refeeding with the normal diet, protein synthesis also rose more rapidly (+30% by 1 day) than proteolysis, which increased significantly after 3 days (+60%). These different time courses suggest distinct endocrine signals for these responses. The high rate of protein synthesis and low rate of proteolysis during the first 3 days of refeeding a normal diet to PD rats contributes to the rapid weight gain ("catch-up growth") of such animals.

Non-NASA Center↗
NASA NTRS1986

Isoelectric focusing of dansylated amino acids in immobilized pH gradients

The 21 free amino acids commonly encountered in proteins have been transformed into 'carrier ampholyte' species by reacting their primary amino groups with dansyl chloride. These derivatives can thus be focused in an immobilized pH gradient covering the pH interval 3.1 to 4.1, except for arginine, which still retains a pI of 8.8. Due to their inherent fluorescence, the dansyl derivatives are revealed in UV light, with a sensitivity of the order of 2-4 ng/sq mm. All nearest neighbors are separated except for the following couples: Asn-Gln, Gly-Thr, Val-Ile and Cys-Cys2, with a resolving power, in a Delta(pI) scale, of the order of 0.0018 pH units. Except for a few cases (notably the aromatic amino acids), the order of pI values is well correlated with the pK values of carboxyl groups, suggesting that the latter are not altered by dansylation. From the set of pK(COOH)-pI values of the different amino acids, the pK of the tertiary amino group in the dansyl label has been calculated to be 5.11 + or - 0.06. Knowing the pK of the amino-dansyl and the pI of the excess, free dansyl label (pI = 3.34), a pK of 1.57 is derived for its sulfonic acid group.

Bianchi-Bosisio, Adriana↗
NASA NTRS2014

The Effects of Thermal Metamorphism on the Amino Acid Content of the CI-Like Chondrite Y-86029

Carbonaceous chondrites con-tain a diverse suite of amino acids that varies in abundance and structural diversity depending on the degree of aqueous alteration and thermal histo-ry that the parent body experienced [1 - 3]. We recently determined the amino acid contents of several fragments of the Sutter's Mill CM2 chon-drite [4]. In contrast with most other CM2 chon-drites, the Sutter's Mill meteorites showed minimal evidence for the presence of indigenous amino acids. A notable difference between the Sutter's Mill meteorites and other CM2 chondrites are that the Sutter's Mill stones were heated to tempera-tures of 150 - 400 C [4], whereas most other CM2 chondrites do not show evidence for thermal met-amorphism [5]. Because empirical studies have shown that amino acids rapidly degrade in aqueous solutions above 150 C and the presence of miner-als accelerates this degradation [6], a plausible explanation for the lack of amino acids observed in the Sutter's Mill meteorites is that they were destroyed during metamorphic alteration. Fewer CI chondrites have been analyzed for amino acids because only a small number of these meteorites have been recovered. Nevertheless, indigenous amino acids have been reported in the CI chondrites Ivuna and Orgueil [7]. Here we report on the amino acid analysis of the CI-like chondrite, Yamato 86029 (Y-86029; sample size of 110 mg). Just as the Sutter's Mill meteorites were thermally metamporphosed CM2 chondrites, Y-86029 has experienced thermal metamorphism at higher temperatures than Orgueil and Ivuna (normal CI chondrites) experienced, possibly up to 600 C [8].

Burton, A. S.↗
NASA NTRS1995

Evolution of the biosynthesis of the branched-chain amino acids

The origins of the biosynthetic pathways for the branched-chain amino acids cannot be understood in terms of the backwards development of the present acetolactate pathway because it contains unstable intermediates. We propose that the first biosynthesis of the branched-chain amino acids was by the reductive carboxylation of short branched chain fatty acids giving keto acids which were then transaminated. Similar reaction sequences mediated by nonspecific enzymes would produce serine and threomine from the abundant prebiotic compounds glycolic and lactic acids. The aromatic amino acids may also have first been synthesized in this way, e.g. tryptophan from indole acetic acid. The next step would have been the biosynthesis of leucine from alpha-ketoisovalerc acid. The acetolactate pathway developed subsequently. The first version of the Krebs cycle, which was used for amino acid biosynthesis, would have been assembled by making use fo the reductive carboxylation and leucine biosynthesis enzymes, and completed with the development of a single new enzyme, succinate dehydrogenase. This evolutionary scheme suggests that there may be limitations to inferring the origins of metabolism by a simple back extrapolation of current pathways.

Keefe, Anthony D.↗
NASA NTRS2005

Sensitive Amino Acid Composition and Chirality Analysis with the Mars Organic Analyzer (MOA)

Detection of life on Mars requires definition of a suitable biomarker and development of sensitive yet compact instrumentation capable of performing in situ analyses. Our studies are focused on amino acid analysis because amino acids are more resistant to decomposition than other biomolecules, and because amino acid chirality is a well-defined biomarker. Amino acid composition and chirality analysis has been previously demonstrated in the lab using microfabricated capillary electrophoresis (CE) chips. To analyze amino acids in the field, we have developed the Mars Organic Analyzer (MOA), a portable analysis system that consists of a compact instrument and a novel multi-layer CE microchip.

Skelley, Alison M.↗