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Results for “AMINO ACID”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 505 records · Page 28
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Prediction of bacterial E3 ubiquitin ligase effectors using reduced amino acid peptide fingerprinting

Background Although pathogenic Gram-negative bacteria lack their own ubiquitination machinery, they have evolved or acquired virulence effectors that can manipulate the host ubiquitination process through structural and/or functional mimicry of host machinery. Many such effectors have been identified in a wide variety of bacterial pathogens that share little sequence similarity amongst themselves or with eukaryotic ubiquitin E3 ligases. Methods To allow identification of novel bacterial E3 ubiquitin ligase effectors from protein sequences we have developed a machine learning approach, the SVM-based Identification and Evaluation of Virulence Effector Ubiquitin ligases (SIEVE-Ub). We extend the string kernel approach used previously to sequence classification by introducing reduced amino acid (RED) alphabet encoding for protein sequences. Results We found that 14mer peptides with amino acids represented as simply either hydrophobic or hydrophilic provided the best models for discrimination of E3 ligases from other effector proteins with a receiver-operator characteristic area under the curve (AUC) of 0.90. When considering a subset of E3 ubiquitin ligase effectors that do not fall into known sequence based families we found that the AUC was 0.82, demonstrating the effectiveness of our method at identifying novel functional family members. Feature selection was used to identify a parsimonious set of 10 RED peptides that provided good discrimination, and these peptides were found to be located in functionally important regions of the proteins involved in E2 and host target protein binding. Our general approach enables construction of models based on other effector functions. We used SIEVE-Ub to predict nine potential novel E3 ligases from a large set of bacterial genomes. SIEVE-Ub is available for download at https://doi.org/10.6084/m9.figshare.7766984.v1 or https://github.com/biodataganache/SIEVE-Ub for the most current version.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Binding and Action of Amino Acid Analogs of Chloramphenicol upon the Bacterial Ribosome

Antibiotic chloramphenicol (CHL) binds with a moderate affinity at the peptidyl transferase center of the bacterial ribosome and inhibits peptide bond formation. As an approach for modifying and potentially improving properties of this inhibitor, we explored ribosome binding and inhibitory activity of a number of amino acid analogs of CHL. We report the L-histidyl analog binds to the ribosome with the affinity exceeding that of CHL by 10 fold. Several of the newly synthesized analogs were able to inhibit protein synthesis and exhibited the mode of action that was distinct from the action of CHL. However, the inhibitory properties of the semi-synthetic CHL analogs did not correlate with their affinity and in general, the amino acid analogs of CHL were less active inhibitors of translation in comparison with the original antibiotic. The X-ray crystal structures of the Thermus thermophilus 70S ribosome in complex with three semi-synthetic analogs showed that CHL derivatives bind at the peptidyl transferase center, where the aminoacyl moiety of the tested compounds established idiosyncratic interactions with rRNA. Although still fairly inefficient inhibitors of translation, the synthesized compounds represent promising chemical scaffolds that target the peptidyl transferase center of the ribosome and potentially are suitable for further exploration.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1995

Utilization of [14C]phenylalanine derived from arylphorin or free amino acid in Manduca sexta pharate adults

The role of arylphorin as a storage protein was studied using 14C-arylphorin. 14C-arylphorin was produced optimally by incubating one-half fat body from Manduca sexta fifth instar larvae at 22 degrees C for 24 h, in 1 ml of medium containing amino acids at 25% of their physiological concentration with [U-14C]-phenylalanine (phe) provided initially without nonlabeled phenylalanine. Nonlabeled phe was provided after 1 h at 16% of its physiological concentration. The specific activity of 14C-arylphorin produced in vitro was 30 times greater than that generated in vivo. Injection of 14C-arylphorin into pharate adults was used to study the distribution of 14C-phe derived from this protein into 14CO2 and tissues for comparison with injection of free 14C-phe during the middle (days 6 to 12 pharate adult) and late (days 12 to 17 pharate adult) stages of adult development. Appearance of 14CO2 from 14C-arylphorin as compared to 14C-phenylalanine showed a slower time course during both the middle and late stages of development, in keeping with the time needed for degradation of the protein. In accord with faster phe turnover near the end of adult development, total 14CO2 production was greater and the retention of 14C in hemolymph and fat body was less compared to the middle stage of development regardless of whether 14C-arylphorin or 14C-phe was injected. In the middle stage of development, the appearance of 14C in the cuticle and head parts was greater, whereas incorporation into abdomen and thorax was less than during the late stage of development. Since the pattern of 14C distribution from 14C-arylphorin and 14C-phe was similar, one major function of arylphorin must be as a storage protein replenishing the supply of free amino acids used for synthesis of adult tissues. These results also suggest a limited contribution of M. sexta arylphorin to formation of the cuticle subsequent to day-6 pharate adult.

Non-NASA Center↗
NASA NTRS1977

Transport in Halobacterium Halobium: Light-Induced Cation-Gradients, Amino Acid Transport Kinetics, and Properties of Transport Carriers

Cell envelope vesicles prepared from H. halobium contain bacteriorhodopsin and upon illumination protons are ejected. Coupled to the proton motive force is the efflux of Na(+). Measurements of Na-22 flux, exterior pH change, and membrane potential, Delta(psi) (with the dye 3,3'-dipentyloxadicarbocyanine) indicate that the means of Na(+) transport is sodium/proton exchange. The kinetics of the pH changes and other evidence suggests that the antiport is electrogenic (H(+)/Na(++ greater than 1). The resulting large chemical gradient for Na(+) (outside much greater than inside), as well as the membrane potential, will drive the transport of 18 amino acids. The I9th, glutamate, is unique in that its accumulation is indifferent to Delta(psi): this amino acid is transported only when a chemical gradient for Na(+) is present. Thus, when more and more NaCl is included in the vesicles glutamate transport proceeds with longer and longer lags. After illumination the gradient of H+() collapses within 1 min, while the large Na(+) gradient and glutamate transporting activity persists for 10- 15 min, indicating that proton motive force is not necessary for transport. A chemical gradient of Na(+), arranged by suspending vesicles loaded with KCl in NaCl, drives glutamate transport in the dark without other sources of energy, with V(sub max) and K(sub m) comparable to light-induced transport. These and other lines of evidence suggest that the transport of glutamate is facilitated by symport with Na(+), in an electrically neutral fashion, so that only the chemical component of the Na(+) gradient is a driving force.

Lanyi, Janos K.↗
NASA NTRS2003

The Infrared Spectrum of Matrix Isolated Aminoacetonitrile: A Precursor to the Amino Acid Glycine

We present infrared (IR) spectral data from matrix isolation experiments and density functional theory calculations on the pre-biologically interesting molecule aminoacetonitrile, a precursor to glycine. We find that this nitrile has an unusually weak nitrile (C=N) stretch in the infrared, in contrast to expectations based on measurements and models of other nitriles under astrophysical conditions. The absence of an observable nitrile absorption feature in the infrared will make the IR search for this molecule considerably more difficult, and will raise estimates of upper limits on nitriles in interstellar and outer Solar System ices. This is also of relevance to assessing the formation routes of the amino acid glycine, since aminoacetonitrile is the putative precursor to glycine via the Strecker synthesis, the mechanism postulated to have produced the amino acids in meteorites.

Bernstein, Max P.↗
DOE OSTI2020

Natively oxidized amino acid residues in the spinach PS I-LHC I supercomplex

Reactive oxygen species (ROS) production is an unavoidable byproduct of electron transport under aerobic conditions. Photosystem II (PS II), the cytochrome b 6 /ƒ complex and Photosystem I (PS I) are all demonstrated sources of ROS. It has been proposed that PS I produces substantial levels of a variety of ROS including O$_{2}^{·-}$, 1 O 2 , H 2 O 2 and, possibly, ∙OH, however, the site(s) of ROS production within PS I has been the subject of significant debate. We hypothesize that amino acid residues close to the sites of ROS generation will be more susceptible to oxidative modification than distant residues. In this study, we have identified oxidized amino acid residues in spinach PS I which was isolated from field-grown spinach. The modified residues were identified by high-resolution tandem mass spectrometry. As expected, many of the modified residues lie on the surface of the complex. However, a well-defined group of oxidized residues, both buried and surface-exposed, lead from the chl a’ of P 700 to the surface of PS I. These residues (PsaB: 609 F, 611 E, 617 M, 619 W, 620 L, and PsaF: 139 L, 142 A, 143 D) may identify a preferred route for ROS, probably 1 O 2 , to egress the complex from the vicinity of P 700 . Additionally, two buried residues located in close proximity to A1B (PsaB: 712 H and 714 S) were modified, which may be consistent with A 1B being a source of O$_{2}^{·-}$. Surprisingly, no oxidatively modified residues were identified in close proximity to the 4Fe-FS clusters F X , F A or F B . These cofactors had been identified as a principal targets for ROS damage in the photosystem. Finally, a large number of residues located in the hydrophobic cores of Lhca1-Lhca4 are oxidatively modified. These appear to be the result of 1 O 2 production by the distal antennae for the photosystem.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

A novel eight amino acid insertion contributes to the hemagglutinin cleavability and the virulence of a highly pathogenic avian influenza A (H7N3) virus in mice

In 2012, an avian influenza A H7N3 (A/Mexico/InDRE7218/2012; Mx/7218) virus was responsible for two confirmed cases of human infection and led to the death or culling of more than 22 million chickens in Jalisco, Mexico. Interestingly, this virus acquired an 8-amino acid (aa)-insertion (..PENPK-DRKSRHRR-TR/GLF) near the hemagglutinin (HA) cleavage site by nonhomologous recombination with host rRNA. It remains unclear which specific residues at the cleavage site contribute to the virulence of H7N3 viruses in mammals. Using loss-of-function approaches, we generated a series of cleavage site mutant viruses by reverse genetics and characterized the viruses in vitro and in vivo. We found that the 8-aa insertion and the arginine at position P4 of the Mx/7218 HA cleavage site are essential for intracellular HA cleavage in 293T cells, but have no effect on the pH of membrane fusion. However, we identified a role for the histidine residue at P5 position in viral fusion pH. In mice, the 8-aa insertion is required for Mx/7218 virus virulence; however, the basic residues upstream of the P4 position are dispensable for virulence. Overall, our study provides the first line of evidence that the insertion in the Mx/7218 virus HA cleavage site confers its intracellular cleavability, and consequently contributes to enhanced virulence in mice. - Highlights: • An avian influenza H7N3 virus acquired a unique 8-amino acid (aa) insertion. • The role of specific basic residues in the HA insertion in viral pathogenesis was determined. • In mice, the 8-aa insertion is required for H7N3 virus virulence. • The R residue at position P4 is essential for HA intracellular cleavage and virus virulence.

60 APPLIED LIFE SCIENCES↗
NASA NTRS2010

Searching for Amino Acids in Meteorites and Comet Samples

Chemistry plays an important role in the interdisciplinary field of astrobiology, which strives to understand the origin, distribution, and evolution of life throughout the universe. Chemical techniques are used to search for and characterize the basic ingredients for life, from the elements through simple molecules and up to the more complex compounds that may serve as the ingredients for life. The Astrobiology Analytical Laboratory at NASA Goddard uses state-of-the-art laboratory analytical instrumentation in unconventional ways to examine extraterrestrial materials and tackle some of the big questions in astrobiology. This talk will discuss some of the instrumentation and techniques used for these unique samples, as well as some of our most interesting results. The talk will present two areas of particular interest in our laboratory: (1) the search for chiral excesses in meteoritic amino acids, which may help to explain the origin of homochirality in life on Earth; and (2) the detection of amino acids and amines in material returned by NASA's Stardust mission, which rendevouzed with a cornet and brought back cometary particles to the Earth.

Cook, Jamie Elsila↗
DOE OSTI2018

Thermal stability of the complex of pyrene–β-cyclodextrin dimer with aromatic amino acids

Using the method of adsorption spectroscopy, the temperature dependence of the electronic absorption spectra of the fluorescent chemosensor (CS), based on the supramolecular pyrene–2β-cyclodextrin complex (Pyr@2βCD, PCD), was studied in the absence and in the presence of phenylalanine (Phe). The application of CS, where pyrene serves as a fluorescent probe, is based on the ability of CS to form the inclusion complexes with small organic molecules as well as with aromatic amino acids (AA) such as Phe, tryptophan (Trp), tyrosine (Tyr), and histidine (His) in aqueous solutions. Upon heating to 55 °C, the PCD complex in the presence of Phe shows a higher stability as compared to that in the absence of Phe. The molecular dynamics simulation was applied to study the thermal stability of PCD and its complexes with the above AAs in water. The PCD complex exists in two configurations. In configuration 1 the planar Pyr molecule lies in the equatorial plane of the βCD dimer, the plane of Pyr is nearly perpendicular to the vertical axis of the dimer 2βCD, and water fills up the empty part of the cavity. In configuration 2, the plane of Pyr is inclined with respect to the axis of the 2βCD dimer by ~30°. The PCD complex initially prepared in state 1 is spontaneously transformed into state 2 and remains stable up to the boiling temperature. The transition of PCD from the form 1 to 2 is provided by fluctuations in water content in its cavities. The inclusion complexes of amino acids 2AA@PCD exist in a single conformation 1. Complexes of PCD with Trp and Phe are stable up to the boiling temperature, i.e., these AAs are preserved within the PCD cavities even at the elevated temperature. The complex with Tyr decays at 60 °C, and the complex with His is unstable at room temperature and above.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Site-Directed Mutagenesis of HgcA and HgcB Reveals Amino Acid Residues Important for Mercury Methylation

Methylmercury is a potent neurotoxin that is produced by anaerobic microorganisms from inorganic mercury by a recently discovered pathway. A two-gene cluster, consisting of hgcA and hgcB, encodes two of the proteins essential for this activity. hgcA encodes a corrinoid protein with a strictly conserved cysteine proposed to be the ligand for cobalt in the corrinoid cofactor, whereas hgcB encodes a ferredoxin-like protein thought to be an electron donor to HgcA. Deletion of either gene eliminates mercury methylation by the methylator Desulfovibrio desulfuricans ND132. Here, site-directed mutants of HgcA and HgcB were constructed to determine amino acid residues essential for mercury methylation. Mutations of the strictly conserved residue Cys93 in HgcA, the proposed ligand for the corrinoid cobalt, to Ala or Thr completely abolished the methylation capacity, but a His substitution produced measurable methylmercury. Mutations of conserved amino acids near Cys93 had various impacts on the methylation capacity but showed that the structure of the putative “cap helix” region harboring Cys93 is crucial for methylation function. In the ferredoxin-like protein HgcB, only one of two conserved cysteines found at the C terminus was necessary for methylation, but either cysteine sufficed. An additional, strictly conserved cysteine, Cys73, was also determined to be essential for methylation. Ultimately, this study supports the previously predicted importance of Cys93 in HgcA for methylation of mercury and reveals additional residues in HgcA and HgcB that facilitate the production of this neurotoxin.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2016

Organic Analysis in the Miller Range 090657 CR2 Chondrite: Part 2 Amino Acid Analyses

Primitive carbonaceous chondrites contain a wide variety of organic material, ranging from soluble discrete molecules to insoluble, unstructured kerogen-like components, as well as structured nano-globules of macromolecular carbon. The relationship between the soluble organic molecules, macromolecular organic material, and host minerals are poorly understood. Due to the differences in extractability of soluble and insoluble organic materials, the analysis methods for each differ and are often performed independently. The combination of soluble and insoluble analyses, when performed concurrently, can provide a wider understanding of spatial distribution, and elemental, structural and isotopic composition of organic material in primitive meteorites. Using macroscale extraction and analysis techniques in combination with in situ microscale observation, we have been studying both insoluble and soluble organic material in the primitive CR2 chondrite Miller Range (MIL) 090657. In accompanying abstracts (Cao et al. and Messenger et al.) we discuss insoluble organic material in the samples. By performing the consortium studies, we aim to improve our understanding of the relationship between the meteorite minerals and the soluble and insoluble organic phases and to delineate which species formed within the meteorite and those that formed in nebular or presolar environments. In this abstract, we present the results of amino acid analyses of MIL 090657 by ultra performance liquid chromatography with fluorescence detection and quadrupole-time of flight mass spectrometry. Amino acids are of interest because they are essential to life on Earth, and because they are present in sufficient structural, enantiomeric and isotopic diversity to allow insights into early solar system chemical processes. Furthermore, these are among the most isotopically anomalous species, yet at least some fraction are thought to have formed by aqueously-mediated processes during parent body alteration.

Burton, A. S.↗