Thermal synthesis of natural amino-acids from a postulated primitive terrestial atmosphere
Synthesis of natural amino acids with thermal energy for biochemical origin study
AMINO ACID↗
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Cometary Amino Acids from the STARDUST Mission
NASA's Stardust spacecraft returned samples from comet 81 P/WiId 2 to Earth in January 2006. Examinations of the organic compounds in cometary samples can reveal information about the prebiotic organic inventory present on the early Earth and within the early Solar System, which may have contributed to the origin of life. Preliminary studies of Stardust material revealed the presence of a suite of organic compounds including several amines and amino acids, but the origin of these compounds (cometary vs. terrestrial contamination) could not be identified. We have recently measured the carbon isotopic ratios of these amino acids to determine their origin, leading to the first detection of a cometary amino acid.
Cook, Jamie Elsila↗
Innovative use of CaO in combination with amino acid salt to convert CO 2 as CaCO 3 nanoparticles under mild pH and low temperature
The increasing demand for sustainable CO 2 management has driven the development of innovative methods that can convert point source CO 2 into value-added products. In this study, CaO in combination with amino acid salt was used to convert CO 2 into CaCO 3 nanoparticles. Different from the conventional method where CO 2 diffusion presents a major challenge in reacting with CaO to form CaCO 3 , amino acid salt solvent was applied to absorb CO 2 first and then rapidly reacted with CaO to form CaCO 3 nanoparticles (∼50 nm) at a low temperature (e.g., 60 °C). Our experiments showed that at a glycine (Gly)/NaOH ratio of 2:1 or 3:1, the solution pH values during the CO 2 absorption and conversion were about 8–9 at 60 °C, while at a ratio of 1:1, the solution pH values were about 9–11; without Gly, the solution pH values were about 12. Gly-optimized solvent substantially reduced corrosion risk to reactors. In addition, the use of amino acid (i.e., Gly) led to much smaller CaCO 3 particles, distinctly different chemical phases, and fundamentally different chemical reactions. Moreover, in the presence of Gly, the solution pH was completely reversed and the solution was regenerated for cyclic use when CaO was added. The solvent was recyclable and reusable, highlighting the cost-effectiveness and sustainability of this approach. The Gly-modulated CaCO 3 nanoparticles may have significant potential for industrial applications in the biomedicine, construction, plastics, and rubber industries.
36 MATERIALS SCIENCE↗
Asymmetric synthesis of alpha-amino acids by the strecker synthesis.
Asymmetric synthesis of alpha-amino acids by strecker synthesis, including production of optically active l-analine
AMINO ACID↗
Copolymerization of the Leuchs anhydrides of the eighteen amino acids common to protein
Copolymerization of Leuchs anhydrides of eighteen amino acids common to protein
PROTEIN↗
Solvation thermodynamics of amino acid side chains on a short peptide backbone
The hydration process of side chain analogue molecules differs from that of the actual amino acid side chains in peptides and proteins owing to the effects of the peptide backbone on the aqueous solvent environment. A recent molecular simulation study has provided evidence that all nonpolar side chains, attached to a short peptide backbone, are considerably less hydrophobic than the free side chain analogue molecules. In contrast to this, the hydrophilicity of the polar side chains is hardly affected by the backbone. To analyze the origin of these observations, we here present a molecular simulation study on temperature dependent solvation free energies of nonpolar and polar side chains attached to a short peptide backbone. The estimated solvation entropies and enthalpies of the various amino acid side chains are compared with existing side chain analogue data. The solvation entropies and enthalpies of the polar side chains are negative, but in absolute magnitude smaller compared with the corresponding analogue data. The observed differences are large; however, owing to a nearly perfect enthalpy-entropy compensation, the solvation free energies of polar side chains remain largely unaffected by the peptide backbone. We find that a similar compensation does not apply to the nonpolar side chains; while the backbone greatly reduces the unfavorable solvation entropies, the solvation enthalpies are either more favorable or only marginally affected. This results in a very small unfavorable free energy cost, or even free energy gain, of solvating the nonpolar side chains in strong contrast to solvation of small hydrophobic or nonpolar molecules in bulk water. The solvation free energies of nonpolar side chains have been furthermore decomposed into a repulsive cavity formation contribution and an attractive dispersion free energy contribution. We find that cavity formation next to the peptide backbone is entropically favored over formation of similar sized nonpolar side chain cavities in bulk water, in agreement with earlier work in the literature on analysis of cavity fluctuations at nonpolar molecular surfaces. The cavity and dispersion interaction contributions correlate quite well with the solvent accessible surface area of the nonpolar side chains attached to the backbone. This correlation however is weak for the overall solvation free energies owing to the fact that the cavity and dispersion free energy contributions are almost exactly cancelling each other.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Syntheses of Optically Active Alpha-amino Acids from Alpha-keto Acids by Hydrogenolytic Asymmetric Transamination
Syntheses of optically active alpha-amino acids from alpha-keto acids by hydrogenolytic asymmetric transamination
AMINO ACID↗
Branched-chain amino acid specialization drove diversification within Calditenuaceae ( Caldarchaeia ) and enables their cultivation
Many thermophiles that are abundant in high-temperature geothermal systems have never been cultivated and are poorly understood, including deeply branching members of the archaeal phylum Thermoproteota. Here, we describe the genome-guided cultivation of one such organism, Calditenuis ramacidaminiphagus, and show that it has evolved a heterotrophic metabolism focused on branched-chain amino acids (BCAAs). Initially, fluorescence in situ hybridization and nanoscale secondary ion mass spectrometry (FISH-nanoSIMS) showed that Cal. ramacidaminiphagus assimilated amino acids rapidly in casamino acid-amended enrichment cultures. Metagenome and metaproteome analyses showed a high abundance and expression of BCAA transporter genes, suggesting a BCAA-focused metabolism. This inference was supported by the subsequent enrichment of Cal. ramacidaminiphagus in BCAA-fed cultures, reaching 2.66×10 6 cells/mL and 48.7% of the community, whereas it was outcompeted when polar amino acids were included. Metabolic reconstruction and metaproteomics suggest that BCAAs are channeled into the mevalonate pathway for lipid biosynthesis and fuel ATP production through the TCA cycle coupled with aerobic respiration and through production of branched-chain organic acids by overflow metabolism. Ancestral state reconstructions and phylogenetic analyses of 62 Caldarchaeales genomes revealed multiple horizontal transfers of BCAA transporters to the ancestor of the genus Calditenuis. Our study highlights the crucial role of BCAAs in the early evolution and niche of this genus, and suggests a high degree of resource partitioning even within low-diversity thermophilic communities.
Biological and medical sciences↗
The Thermal Synthesis of Amino Acids from a Hypothetically Primitive Terrestrial Atmosphere.
Thermal synthesis of amino acids from hypothetically primitive terrestrial atmosphere
SYNTHESIS↗
Formation of amino-acids by thermal decomposition of formamide - Oligomerization of hydrogen cyanide.
Amino acid formation by formamide thermal decomposition, noting support for hydrogen cyanide oligomerization hypothesis
HYDROGEN CYANIDE↗
Amino Acids in the Antarctic Martian Meteorite MIL03346
The report by McKay et al. that the Martian meteorite ALH84001 contains evidence for life on Mars remains controversial. Of central importance is whether ALH84001 and other Antarctic Martian meteorites contain endogenous organic compounds. In any investigation of organic compounds possibly derived from Mars it is important to focus on compounds that play an essential role in biochemistry as we know it and that have properties such as chirality which can be used to distinguish between biotic versus abiotic origins. Amino acids are one of the few compounds that fulfill these requirements. Previous analyses of the Antarctic Martian meteorites ALH84001 and EETA79001 have shown that these meteorites contain low levels of terrestrial amino acid contamination derived from Antarctic ice meltwater. Here we report preliminary amino acid investigations of a third Antarctic Martian meteorite MIL03346 which was discovered in Antarctica during the 2003-04 ANSMET season. Additional information is included in the original extended abstract
Glavin, D. P.↗
High resolution NMR study of T{sub 1} magnetic relaxation dispersion. IV. Proton relaxation in amino acids and Met-enkephalin pentapeptide
Nuclear Magnetic Relaxation Dispersion (NMRD) of protons was studied in the pentapeptide Met-enkephalin and the amino acids, which constitute it. Experiments were run by using high-resolution Nuclear Magnetic Resonance (NMR) in combination with fast field-cycling, thus enabling measuring NMRD curves for all individual protons. As in earlier works, Papers I–III, pronounced effects of intramolecular scalar spin-spin interactions, J-couplings, on spin relaxation were found. Notably, at low fields J-couplings tend to equalize the apparent relaxation rates within networks of coupled protons. In Met-enkephalin, in contrast to the free amino acids, there is a sharp increase in the proton T{sub 1}-relaxation times at high fields due to the changes in the regime of molecular motion. The experimental data are in good agreement with theory. From modelling the relaxation experiments we were able to determine motional correlation times of different residues in Met-enkephalin with atomic resolution. This allows us to draw conclusions about preferential conformation of the pentapeptide in solution, which is also in agreement with data from two-dimensional NMR experiments (rotating frame Overhauser effect spectroscopy). Altogether, our study demonstrates that high-resolution NMR studies of magnetic field-dependent relaxation allow one to probe molecular mobility in biomolecules with atomic resolution.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
The thermal synthesis of amino acids from a hypothetically primitive terrestrial atmosphere.
Thermal synthesis of amino acids from methane- ammonia-water mixture passing through Earth-crust materials
AMINO ACID↗
Extraterrestrial hydroxy amino acids in CM and CR carbonaceous chondrites
The abundances, distributions, and enantiomeric ratios of a family of three- and four-carbon hydroxy amino acids (HAAs) were investigated in extracts of five CM and four CR carbonaceous chondrites by gas chromatography-mass spectrometry analyses. HAAs were detected in both the acid hydrolysates of the hot water extracts and the 6 M HCl extracts of all the CM and CR chondrites analyzed here with total hot water and HCl extractable HAA concentrations ranging from 6.94 to 315 nmol/g. The HAA analyses performed in this study revealed: (1) the combined (hot water + HCl) extracts of CR2 chondrites contained greater abundances of α-HAAs than that of CM2 chondrites and (2) the combined extracts of CM and CR chondrites contained roughly similar abundances of β- and γ-HAAs. Application of the new GC-MS method developed here resulted in the first successful chromatographic resolution of the enantiomers of an α-dialkyl HAA, d,l-α-methylserine, in carbonaceous chondrite extracts. Meteoritic α-methylserine was found to be mostly racemic within error and did not show l-enantiomeric excesses correlating with the degree of aqueous alteration, a phenomenon observed in meteoritic isovaline, another α-dialkyl amino acid. The HAAs identified in CM and CR chondrite extracts could have been produced during parent body alteration from the Strecker cyanohydrin reaction (for α-HAAs) and an ammonia-involved formose-like reaction (for β-, and γ-HAAs).
Amino acid(s)↗
Daily rhythms in the concentrations of various amino acids in human plasma.
Daily rhythms in concentrations of various amino acids in human plasma
BLOOD PLASMA↗
Highly efficient peptide formation from N-acetylaminoacyl-AMP anhydride and free amino acid
The kinetics of formation of the N-blocked dipeptide, N-acetylglycylglycine, from N-acetylglycyl adenylate anhydride and glycine in aqueous solution at 25 C, and at various PH's are reported. The reaction is of interest in that over a physiologically relevant pH range (6-8), peptide synthesis proceeds more rapidly than hydrolysis, even at those pH's at which this compound becomes increasingly susceptible to base-catalyzed hydrolysis. Under similar conditions, the corresponding unblocked aminoacyl adenylate anhydrides are considerably more unstable, and undergo appreciable hydrlysis in the presence of free amino acid. Because N-blocked aminoacyl adenylate anhydrides serve as model compounds of peptidyl adenylate anhydrides, these results suggest that primitive amino acid polymerization systems may have operated by cyclic reactivation of the peptidyl carboxyl group, rather than that of the incoming amino acid.
Mullins, D. W., Jr.↗
Amino acids in a Fischer Tropsch type synthesis
One postulation is described for the presence of organic compounds in meteorites which states that they were formed during the condensation of the solar nebula. A viable laboratory simulation of these conditions can be modeled after the industrial Fischer Tropsch reaction, which is known to produce organic compounds called hydrocarbons. In this simulation, a mixture of carbon monoxide, hydrogen and ammonia is heated in the presence of iron meteorite. The reaction products for amino acids, a class of organic compounds important to life, were examined. A large number of these compounds is found in meteorites and other chemical evolution experiments, but only small quantities of a few amino acids were found in the present simulation work. These results are at odds with the existing literature in which many amino acids were reported.
Brown, D. L.↗
NCAP: Noncanonical Amino Acid Parameterization Software for CHARMM Potentials
Noncanonical Amino Acids (NCAAs) provide numerous avenues for introduction of novel functionality to peptides and proteins. NCAAs can be incorporated through solid phase synthesis or genetic code expansion in conjugation with heterologous expression of the encoded protein modification. Due to the difficulty of synthesis, wide chemical space and lack of empirically resolved structures modeling the effects of NCAA mutation is critical for rational protein design. To evaluate the structural and functional perturbations NCAAs introduce we utilize molecular potentials that describe the forces in protein structure. Most potentials such as CHARMM are designed to model canonical residues but can be parameterized in include novel NCAAs. Here, in this work, we introduce NCAP a software package to generate CHARMM compatible parameters from quantum chemical calculation. Unlike currently available tools NCAP is designed to recognize NCAA structure and automatically bridge the gap between DFT calculations and potential parameters. For our software we discuss workflow, validation against canonical parameter sets and comparison to published NCAA-protein structures.
59 BASIC BIOLOGICAL SCIENCES↗