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At least 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

ff19SB: Amino-acid specific protein backbone parameters trained against quantum mechanics energy surfaces in solution

Molecular dynamics (MD) simulations have become increasingly popular in studying the motions and functions of biomolecules. The accuracy of the simulation, however, is highly determined by the molecular mechanics (MM) force field (FF), a set of functions with adjustable parameters to compute the potential energies from atomic positions. However, the overall quality of the FF, such as our previously published ff99SB and ff14SB, can be limited by assumptions that were made years ago. In the updated model presented here (ff19SB), we have significantly improved the backbone profiles for all 20 amino acids. We fit coupled Φ/ψ parameters using 2D Φ/ψ conformational scans for multiple amino acids, using as reference data the entire 2D quantum mechanics (QM) energy surface. We address the polarization inconsistency during dihedral parameter fitting by using both QM and MM in solution. Finally, we examine possible dependency of the backbone fitting on side chain rotamer. To extensively validate ff19SB parameters, we have performed a total of ~5 milliseconds MD simulations in explicit solvent. Here, our results show that after amino-acid specific training against QM data with solvent polarization, ff19SB not only reproduces the differences in amino acid specific Protein Data Bank (PDB) Ramachandran maps better, but also shows significantly improved capability to differentiate amino acid dependent properties such as helical propensities. We also conclude that an inherent underestimation of helicity is present in ff14SB, which is (inexactly) compensated by an increase in helical content driven by the TIP3P bias toward overly compact structures. In summary, ff19SB, when combined with a more accurate water model such as OPC, should have better predictive power for modeling sequence-specific behavior, protein mutations, and also rational protein design.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2016

DEUTERIUM FRACTIONATION DURING AMINO ACID FORMATION BY PHOTOLYSIS OF INTERSTELLAR ICE ANALOGS CONTAINING DEUTERATED METHANOL

Deuterium (D) atoms in interstellar deuterated methanol might be distributed into complex organic molecules through molecular evolution by photochemical reactions in interstellar grains. In this study, we use a state-of-the-art high-resolution mass spectrometer coupled with a high-performance liquid chromatography system to quantitatively analyze amino acids and their deuterated isotopologues formed by the photolysis of interstellar ice analogs containing singly deuterated methanol CH{sub 2}DOH at 10 K. Five amino acids (glycine, α -alanine, β -alanine, sarcosine, and serine) and their deuterated isotopologues whose D atoms are bound to carbon atoms are detected in organic residues formed by photolysis followed by warming up to room temperature. The abundances of singly deuterated amino acids are in the range of 0.3–1.1 relative to each nondeuterated counterpart, and the relative abundances of doubly and triply deuterated species decrease with an increasing number of D atoms in a molecule. The abundances of amino acids increase by a factor of more than five upon the hydrolysis of the organic residues, leading to decreases in the relative abundances of deuterated species for α -alanine and β -alanine. On the other hand, the relative abundances of the deuterated isotopologues of the other three amino acids did not decrease upon hydrolysis, indicating different formation mechanisms of these two groups upon hydrolysis. The present study facilitates both qualitative and quantitative evaluations of D fractionation during molecular evolution in the interstellar medium.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

Basic amino acid residues located in the N-terminal region of BEND3 are essential for its nuclear localization

BEN domain-containing protein 3 (BEND3) has recently been reported to function as a heterochromatin-associated protein in transcriptional repression in the nucleus. BEND3 should have nuclear localization signals (NLSs) to localize to the nucleus in light of its molecular weight, which is higher than that allowed to pass through nuclear pore complexes. We here analyzed the subcellular localization of deletion/site-directed mutants of human BEND3 by an immunofluorescence assay in an attempt to identify the amino acids essential for its nuclear localization. We found that three basic amino acid residues located in the N-terminal region of BEND3 (BEND3{sub 56–58}, KRK) are essential, suggesting that these residues play a role as a functional NLS. These results provide valuable information for progressing research on BEND3. - Highlights: • BEND3 localizes to the nucleus. • The N-terminal 60 amino acids region of BEND3 contains NLS. • Amino acids located between 56 and 58 of BEND3 (KRK) are part of NLS. • KRK motif is highly conserved among BEND3 homologs.

60 APPLIED LIFE SCIENCES↗
NASA NTRS2009

On the Search for the Amino Acids on the Lunar Surface as it Relates to Other Extraterrestrial Bodies

The early search for the amino acids on the lunar surface fines indicated such a low amount of the amino acids that it was deemed insignifi cant. While the later studies seemed to depart in some ways from the earlier results, they were not pursued. In this paper we critically ev aluate the results from the Apollo missions from the new perspective with considerations of the sensitivity of the instrumentation availabl e at the time. We discuss the possible relevance of the lunar results to the findings of the amino acids on the surfaces of other extraterrestrial bodies, such as Mars.

Hoover, Richard B.↗
NASA NTRS1991

Modification of amino acids at shock pressures of 3 to 30 GPA: Initial results

Since the discovery of amino acids in the Murchison meteorite, much speculation has focused on their origin and subsequent alteration, including the possible role of secondary processes, both terrestrial and extraterrestrial. As collisional processes and associated shock waves seem to have affected the silicate portions of many primitive meteorites, a mixture of powdered Allende (125-150 m grain size) and nine synthetic amino acids (six protein and three nonprotein) were subjected to controlled shock pressures from 3 to 30 GPa to determine the effect of shocks on amino acid survivability. Preliminary characterizations of the recovered shock products are presented.

Peterson, Etta↗
DOE OSTI2020

Host cells and methods for oxidizing aromatic amino acids

The present invention provides for a method of producing an oxidation product of an aromatic amino acid in a genetically modified host cell. The method comprises culturing the genetically modified host cell under a suitable condition such that the culturing results in the genetically modified host cell producing oxidation product of an aromatic amino acid. The host cell comprises an enzyme capable of catalyzing the oxidation of aromatic amino acid. In some embodiments, the host cell is capable of biosynthesizing BH4 or MH4 from GTP.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2015

Effect of a Synchrotron X-ray Microtomography Imaging Experiment on the Amino Acid Content of a CM Chondrite

X-ray microcomputed tomography and synchrotron X-ray microcomputed tomography (μCT) are becoming popular tools for the reconnaissance imaging of chondrites. However, there are occasional concerns that the use of μCT may be detrimental to organic components of a chondrite. Soluble organic compounds represent ~2–10% of the total solvent extractable carbon in CI and CM carbonaceous chondrites and amino acids are among the most abundant compounds in the soluble organic fraction. We irradiated two samples of the Murchison CM2 carbonaceous chondrite under conditions slightly harsher (increased beam exposure time) than those typically used for x-ray μCT imaging experiments to determine if detectable changes in the amino acid abundance and distribution relative to a nonexposed control sample occurred. After subjecting two meteorite portions to ionizing radiation dosages of 1.1 kiloGray (kGy) and 1.2 kGy with 48.6 and 46.6 keV monochromatic X-rays, respectively, we analyzed the amino acid content of each sample. Within analytical errors, we found no differences in the amino acid abundances or enantiomeric ratios when comparing the control samples (nonexposed Murchison) and the irradiated samples. We show with calculations that any sample heating due to x-ray exposure is negligible. We conclude that a monochromatic synchrotron X-ray μCT experiment at beamline 13-BM-D of the Advanced Photon Source, which imparts ~1 kGy doses, has no detectable effect on the amino acid content of a carbonaceous chondrite. These results are important for the initial reconnaissance of returned samples from the OSIRIS-REx and Hayabusa 2 asteroid sample return missions.

Jon M. Friedrich↗
NASA NTRS2013

On-Chip Microfluidic Components for In Situ Analysis, Separation, and Detection of Amino Acids

The Astrobiology Analytical Laboratory at GSFC has identified amino acids in meteorites and returned cometary samples by using liquid chromatography-electrospray ionization time-of-flight mass spectrometry (LCMS). These organic species are key markers for life, having the property of chirality that can be used to distinguish biological from non-biological amino acids. One of the critical components in the benchtop instrument is liquid chromatography (LC) analytical column. The commercial LC analytical column is an over- 250-mm-long and 4.6-mm-diameter stainless steel tube filled with functionized microbeads as stationary phase to separate the molecular species based on their chemistry. Miniaturization of this technique for spaceflight is compelling for future payloads for landed missions targeting astrobiology objectives. A commercial liquid chromatography analytical column consists of an inert cylindrical tube filled with a stationary phase, i.e., microbeads, that has been functionalized with a targeted chemistry. When analyte is sent through the column by a pressurized carrier fluid (typically a methanol/ water mixture), compounds are separated in time due to differences in chemical interactions with the stationary phase. Different species of analyte molecules will interact more strongly with the column chemistry, and will therefore take longer to traverse the column. In this way, the column will separate molecular species based on their chemistry. A lab-on-chip liquid analysis tool was developed. The microfluidic analytical column is capable of chromatographically separating biologically relevant classes of molecules based on their chemistry. For this analytical column, fabrication, low leak rate, and stationary phase incorporation of a serpentine microchannel were demonstrated that mimic the dimensions of a commercial LC column within a 5 10 1 mm chip. The microchannel in the chip has a 75- micrometer-diameter oval-shaped cross section. The serpentine microchannel has four different lengths: 40, 60, 80, and 100 mm. Functionized microbeads were filled inside the microchannel to separate molecular species based on their chemistry.

Zheng, Yun↗
NASA NTRS1972

Amino acid analyses of Apollo 14 samples.

Detection limits were between 300 pg and 1 ng for different amino acids, in an analysis by gas-liquid chromatography of water extracts from Apollo 14 lunar fines in which amino acids were converted to their N-trifluoro-acetyl-n-butyl esters. Initial analyses of water and HCl extracts of sample 14240 and 14298 samples showed no amino acids above background levels.

Gehrke, C. W.↗
NASA NTRS2008

Compound-Specific Isotope Analysis of Amino Acids for Stardust-Returned Samples

Significant portions of the early Earth's prebiotic organic inventory , including amino acids, could have been delivered to the Earth's sur face by comets and their fragments. Analysis of comets via spectrosc opic observations has identified many organic molecules, including me thane, ethane, arnmonia, cyanic acid, formaldehyde, formamide, acetal ehyde, acetonitrile, and methanol. Reactions between these identifie d molecules could allow the formation of more complex organics such a s amino acids. Isotopic analysis could reveal whether an extraterrest rial signature is present in the Stardust-exposed amines and amino ac ids. Although bulk isotopic analysis would be dominated by the EACA contaminant's terrestrial signature, compoundspecific isotope analysi s (CSIA) could determine the signature of each of the other individua l amines. Here, we report on progress made towards CSIA of the amino acids glycine and EACA in Stardustreturned samples.

Cook, Jamie↗
NASA NTRS1990

Comet dust as a source of amino acids at the Cretaceous/Tertiary boundary

It is suggested here that the large amounts of apparently extraterrestrial amino acids detected recently in rocks at the K/T boundary at Stevns Klint, Denmark were actually deposited with the dust from a giant comet trapped in the inner solar system, a fragment of which comprised the K/T impactor. Amino acids or their precursors in the comet dust would have been swept up by the earth both before and after the impact, but any conveyed by the impactor itself would have been destroyed. The observed amino acid layers would thus have been deposited without an impact.

Zahnle, Kevin↗
NASA NTRS1972

Evidence for amino-acids of extraterrestrial origin in the Orgueil meteorite.

The problems of separation of contaminant from indigenous amino-acids in meteorites can be largely overcome by applying gas chromatographic techniques for the separation of D,L enantiomers of amino-acids as their diastereomeric derivatives and the identification of these compounds by gas chromatographic retention times and mass spectral fragmentation patterns. Two samples of Orgueil meteorite were examined. The results show that there are amino-acids indigenous to the Orgueil meteorite in addition to those present as contaminants.

Lawless, J. G.↗
NASA NTRS1993

Comment on 'Summary and implications of reported amino acid concentrations in the Murchison meteorite' by E. L. Shock and M. D. Schulte

A criticism of the claim by Shock and Schulte (1990) that there is a correlation between the amino acid abundances (relative to glycine) in the Murchison meteorite and their aqueous solubilities is presented. Their suggestion that 'the same factors which control the aqueous solubility of many amino acids also control their relative abundances in the Murchison meteorite is argued to be incorrect. It is proposed that even though the water/meteorite ratio would have been less during meteorite aqueous alteration than that in the 100-C laboratory extraction procedure, amino acids are simply too soluble. The distribution of other meteorite organic components such as PAHs may have been affected by alteration because they are only slightly soluble in water and can be easily separated by geochromatographic processes. In their reply Shock and Schulte contend that the critics argue against a point not made in their paper and that their argument was supported with several unsubstantiated assertions, including an unfounded claim that the temperature dependence of amino acid solubilities are 'not greatly different', a misrepresentation of isopiestic studies on concentration solutions as equilibrium solubility measurements.

Miller, Stanley L.↗
DOE OSTI2020

Adaptive laboratory evolution of methylotrophic Escherichia coli enables synthesis of all amino acids from methanol-derived carbon

Recent attempts to create synthetic Escherichia coli methylotrophs identified that de novo biosynthesis of amino acids, in the presence of methanol, presents significant challenges in achieving autonomous methylotrophic growth. Previously engineered methanol-dependent strains required co-utilization of stoichiometric amounts of co-substrates and methanol. As such, these strains could not be evolved to grow on methanol alone. In this work, we have explored an alternative approach to enable biosynthesis of all amino acids from methanol-derived carbon in minimal media without stoichiometric coupling. First, we identified that biosynthesis of threonine was limiting the growth of our methylotrophic E. coli. To address this, we performed adaptive laboratory evolution to generate a strain that grew efficiently in minimal medium with methanol and threonine. Methanol assimilation and growth of the evolved strain were analyzed and, interestingly, we found that the evolved strain synthesized all amino acids, including threonine, from methanol-derived carbon. Here, the evolved strain was then further engineered through overexpression of an optimized threonine biosynthetic pathway. We show that the resulting methylotrophic E. coli strain has a methanol-dependent growth phenotype with homoserine as co-substrate. In contrast to previous methanol-dependent strains, co-utilization of homoserine is not stoichiometrically linked to methanol assimilation. As such, future engineering of this strain and successive adaptive evolution could enable autonomous growth on methanol as the sole carbon source.

13C-labeling analysis↗
DOE OSTI2014

Preexisting compensatory amino acids compromise fitness costs of a HIV-1 T cell escape mutation

Background: Fitness costs and slower disease progression are associated with a cytolytic T lymphocyte (CTL) escape mutation T242N in Gag in HIV-1-infected individuals carrying HLA-B*57/5801 alleles. However, the impact of different context in diverse HIV-1 strains on the fitness costs due to the T242N mutation has not been well characterized. To better understand the extent of fitness costs of the T242N mutation and the repair of fitness loss through compensatory amino acids, we investigated its fitness impact in different transmitted/founder (T/F) viruses. Results: The T242N mutation resulted in various levels of fitness loss in four different T/F viruses. However, the fitness costs were significantly compromised by preexisting compensatory amino acids in (Isoleucine at position 247) or outside (glutamine at position 219) the CTL epitope. Moreover, the transmitted T242N escape mutant in subject CH131 was as fit as the revertant N242T mutant and the elimination of the compensatory amino acid I247 in the T/F viral genome resulted in significant fitness cost, suggesting the fitness loss caused by the T242N mutation had been fully repaired in the donor at transmission. Analysis of the global circulating HIV-1 sequences in the Los Alamos HIV Sequence Database showed a high prevalence of compensatory amino acids for the T242N mutation and other T cell escape mutations. Conclusions: Our results show that the preexisting compensatory amino acids in the majority of circulating HIV-1 strains could significantly compromise the fitness loss due to CTL escape mutations and thus increase challenges for T cell based vaccines.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Energy-Efficient CO 2 Capture from Flue Gas by Absorption with Amino Acids and Crystallization with a Bis-Iminoguanidine

In this work, we report a hybrid solvent/solid-state approach to CO 2 separation from flue gas, consisting of absorption with aqueous glycine or sarcosine amino acids, followed by crystallization of the bicarbonate salt of glyoxal-bis(iminoguanidine) (GBIG), and subsequent solid-state CO 2 release from the bicarbonate crystals. In this process, the GBIG bicarbonate crystallization regenerates the amino acid sorbent at ambient temperature, and the CO 2 is subsequently released by mild heating (120 °C) of the GBIG bicarbonate crystals, which results in quantitative regeneration of GBIG. The cyclic capacities measured from multiple absorption–regeneration cycles are in the range of 0.2–0.3 mol CO 2 /mol amino acid. The regeneration energy of this hybrid solvent/solid-state approach is 24% and 40% lower than the regeneration energy of benchmark industrial sorbents monoethanolamine and sodium glycinate, respectively. Lastly, as the amino acid sorbent is never heated in the hybrid process, its loss through evaporation or degradation is minimized.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗