Engineering Papers⌕ Search

SEARCH · Engineering Papers

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2013

Genetically programmed expression of proteins containing the unnatural amino acid phenylselenocysteine

The invention relates to orthogonal pairs of tRNAs and aminoacyl-tRNA synthetase that can incorporate the unnatural amino acid phenylselenocysteine into proteins produced in eubacterial host cells such as E. coli. The invention provides, for example but not limited to, novel orthogonal aminoacyl-tRNA synthetases, polynucleotides encoding the novel sythetases molecules, methods for identifying and making the novel synthetases, methods for producing containing the unnatural amino acid phenylselenocysteine and translation systems. The invention further provides methods for producing modified proteins (e.g., lapidated proteins) through targeted modification of the phenylselenocysteine residue in a protein.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

Genetically programmed expression of proteins containing the unnatural amino acid phenylselenocysteine

The invention relates to orthogonal pairs of tRNAs and aminoacyl-tRNA synthetases that can incorporate the unnatural amino acid phenylselenocysteine into proteins produced in eubacterial host cells such as E. coli . The invention provides, for example but not limited to, novel orthogonal aminoacyl-tRNA synthetases, polynucleotides encoding the novel synthetase molecules, methods for identifying and making the novel synthetases, methods for producing proteins containing the unnatural amino acid phenylselenocysteine and translation systems. The invention further provides methods for producing modified proteins (e.g., lipidated proteins) through targeted modification of the phenylselenocysteine residue in a protein.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

A Single Amino Acid Change in Nramp6 from Sedum Alfredii Hance Affects Cadmium Accumulation

SaNramp6 in Sedum alfredii encodes a membrane-localized metal transporter. We isolated the SaNramp6h allele from the hyperaccumulating ecotype (HE) of S. alfredii . When this allele was expressed in transgenic yeast and Arabidopsis thaliana , it enhanced their cadmium (Cd) sensitivity by increased Cd transport and accumulation. We isolated another allele, SaNramp6n , from a nonhyperaccumulating ecotype (NHE) of S. alfredii . Amino acid sequence comparisons revealed three amino acid differences between SaNramp6h and SaNramp6n. We investigated the Cd transport activity of the Nramp6 allele, and determined which residues are essential for the transport activity. We conducted structure-function analyses of SaNramp6 based on site-directed mutagenesis and functional assays of the mutants in yeast and Arabidopsis . The three residues that differed between SaNramp6h and SaNramp6n were mutated. Only the L157P mutation of SaNramp6h impaired Cd transport. The other mutations, S218N and T504A, did not affect the transport activity of SaNramp6h, indicating that these residues are not essential for metal selectivity. Transgenic plants overexpressing SaNramp6h L157P showed altered metal accumulation in shoots and roots. Our results suggest that the conserved site L157 is essential for the high metal transport activity of SaNramp6h. This information may be useful for limiting or increasing Cd transport by other plant natural resistance associated macrophage protein (NRAMP) proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Evolution of translation machinery in recoded bacteria enables multi-site incorporation of nonstandard amino acids

Expansion of the genetic code with nonstandard amino acids (nsAAs) has enabled biosynthesis of proteins with diverse new chemistries. However, this technology has been largely restricted to proteins containing a single or few nsAA instances. We describe an in vivo evolution approach in a genomically recoded Escherichia coli strain for the selection of orthogonal translation systems capable of multi-site nsAA incorporation. We evolved chromosomal aminoacyl-tRNA synthetases (aaRSs) with up to 25-fold increased protein production for p-acetyl-L-phenylalanine and p-azido-L-phenylalanine (pAzF). We also evolved aaRSs with tunable specificities for 14 nsAAs, including an enzyme that efficiently charges pAzF while excluding 237 other nsAAs. These variants enabled production of elastin-like-polypeptides with 30 nsAA residues at high yields (~50 mg/L) and high accuracy of incorporation (>95%). This approach to aaRS evolution should accelerate and expand our ability to produce functionalized proteins and sequence-defined polymers with diverse chemistries.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

On the role of α-alumina in the origin of life: Surface-driven assembly of amino acids

We investigate the hypothesis that mineral/water interfaces played a crucial catalytic role in peptide formation by promoting the self-assembly of amino acids. Using classical molecular dynamics simulations, we demonstrate that the α-alumina(0001) surface exhibits an affinity of 4k B Tfor individual glycine or GG dipeptide molecules due to hydrogen bonds. In simulations with multiple glycine molecules, surface-bound glycine enhances further adsorption, leading to the formation of long chains connected by hydrogen bonds between the carboxyl and amine groups of glycine molecules. We find that the likelihood of observing chains longer than 10 glycine units increases by at least five orders of magnitude at the surface compared to the bulk. This surface-driven assembly is primarily due to local high density and alignment with the alumina surface pattern. Together, these results propose a model for how mineral surfaces can induce configuration-specific assembly of amino acids, thereby promoting condensation reactions.

Science & Technology - Other Topics↗
DOE OSTI2018

Influence of isopropylmalate synthase Os IPMS 1 on seed vigour associated with amino acid and energy metabolism in rice

Summary Seed vigour is an imperative trait for the direct seeding of rice. Isopropylmalate synthase ( IPMS ) catalyses the committed step of leucine (Leu) biosynthesis, but its effect on seed vigour remains unclear. In this study, rice Os IPMS 1 and Os IPMS 2 was cloned, and the roles of Os IPMS 1 in seed vigour were mainly investigated. Os IPMS 1 and Os IPMS 2 catalyse Leu biosynthesis, and Leu feedback inhibits their IPMS activities. Disruption of Os IPMS 1 resulted in low seed vigour under various conditions, which might be tightly associated with the reduction of amino acids in germinating seeds. Eleven amino acids that associated with stress tolerance, GA biosynthesis and tricarboxylic acid ( TCA ) cycle were significantly reduced in osipms1 mutants compared with those in wide type ( WT ) during seed germination. Transcriptome analysis indicated that a total of 1209 differentially expressed genes ( DEG s) were altered in osipms1a mutant compared with WT at the early germination stage, wherein most of the genes were involved in glycolysis/gluconeogenesis, protein processing, pyruvate, carbon, fructose and mannose metabolism. Further analysis confirmed that the regulation of Os IPMS 1 in seed vigour involved in starch hydrolysis, glycolytic activity and energy levels in germinating seeds. The effects of seed priming were tightly associated with the mRNA levels of Os IPMS 1 in priming seeds. The Os IPMS 1 might be used as a biomarker to determine the best stop time‐point of seed priming in rice. This study provides novel insights into the function of Os IPMS 1 on seed vigour and should have practical applications in seed priming of rice.

He, Yongqi↗
DOE OSTI2021

Methods of making polypeptides with non-standard amino acids using genomically recoded organisms

A method of making a polypeptide including at least one covalent bond between a pair of reactive side chains of corresponding amino acids, wherein the covalent bond is insensitive to reduction is provided including genetically modifying a genomically recoded organism to express a corresponding synthetase, tRNA or synthetase/tRNA pair for translating mRNA encoding the corresponding amino acids having the reactive side chains into the polypeptide and to express the polypeptide including the at least one pair of the reactive side chains wherein the reactive side chains are oriented near one another when the expressed polypeptide is in a folded configuration, wherein the reactive side chains react to form the covalent bond that is insensitive to reduction.

Church, George M.↗
DOE OSTI2016

Thermodynamics of Hydrophobic Amino Acids in Solution: A Combined Experimental–Computational Study

Here, we present a joint experimental-computational study to quantitatively describe the thermodynamics of hydrophobic leucine amino acids in aqueous solution. X-ray scattering data were acquired at a series of solute and salt concentrations to effectively measure inter-leucine interactions, indicating that a major scattering peak is observed consistently at q = 0.83 Å -1 . Atomistic molecular dynamics simulations were then performed and compared with the scattering data, achieving high consistency at both small and wider scattering angles (q = 0$-$1.5 Å -1 ). This experimental-computational consistence enables a first glimpse of the leucineleucine interacting landscape, where two leucine molecules are aligned mostly in a parallel fashion, as opposed to anti-parallel, but also allows us to derive effective leucine-leucine interactions in solution. Collectively, this combined approach of employing experimental scattering and molecular simulation enables a quantitative characterization on effective inter-molecular interactions of hydrophobic amino acids, critical for protein function and dynamics such as protein folding.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2011

Site specific incorporation of keto amino acids into proteins

Compositions and methods of producing components of protein biosynthetic machinery that include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, and orthogonal pairs of tRNAs/synthetases, which incorporate keto amino acids into proteins are provided. Methods for identifying these orthogonal pairs are also provided along with methods of producing proteins with keto amino acids using these orthogonal pairs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

Site specific incorporation of keto amino acids into proteins

Compositions and methods of producing components of protein biosynthetic machinery that include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, and orthogonal pairs of tRNAs/synthetases, which incorporate keto amino acids into proteins are provided. Methods for identifying these orthogonal pairs are also provided along with methods of producing proteins with keto amino acids using these orthogonal pairs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

In situ visualization of newly synthesized proteins in environmental microbes using amino acid tagging and click chemistry

Summary Here we describe the application of a new click chemistry method for fluorescent tracking of protein synthesis in individual microorganisms within environmental samples. This technique, termed bioorthogonal non‐canonical amino acid tagging ( BONCAT ), is based on the in vivo incorporation of the non‐canonical amino acid L ‐azidohomoalanine ( AHA ), a surrogate for l ‐methionine, followed by fluorescent labelling of AHA ‐containing cellular proteins by azide‐alkyne click chemistry. BONCAT was evaluated with a range of phylogenetically and physiologically diverse archaeal and bacterial pure cultures and enrichments, and used to visualize translationally active cells within complex environmental samples including an oral biofilm, freshwater and anoxic sediment. We also developed combined assays that couple BONCAT with ribosomal RNA (rRNA)‐targeted fluorescence in situ hybridization ( FISH ), enabling a direct link between taxonomic identity and translational activity. Using a methanotrophic enrichment culture incubated under different conditions, we demonstrate the potential of BONCAT‐FISH to study microbial physiology in situ . A direct comparison of anabolic activity using BONCAT and stable isotope labelling by nano‐scale secondary ion mass spectrometry ( 15 NH 3 assimilation) for individual cells within a sediment‐sourced enrichment culture showed concordance between AHA ‐positive cells and 15 N enrichment. BONCAT‐FISH offers a fast, inexpensive and straightforward fluorescence microscopy method for studying the in situ activity of environmental microbes on a single‐cell level.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Self‐assembling Peptides with Internal Ionizable Unnatural Amino Acids: A General Approach to pH‐responsive Peptide Materials

Self‐assembled peptides are an emerging family of biomaterials that show great promise for a range of biomedical and biotechnological applications. Introducing and tuning the pH‐responsiveness of the assembly is highly desirable for improving their biological activities. Inspired by proteins with internal ionizable residues, we report a simple but effective approach to constructing pH‐responsive peptide assembly containing unnatural ionic amino acids with an aliphatic tertiary amine side chain. Through a combined experimental and computational investigation, we demonstrate that these residues can be accommodated and stabilized within the internal hydrophobic compartment of the peptide assembly. The hydrophobic microenvironment shifts their pK a significantly from a basic pH typically found for free amines to a more biologically relevant pH in the weakly acidic range. The pH‐induced ionization and ionization‐dependent self‐assembly and disassembly are thoroughly investigated and correlated with the biological activity of the assembly. This new approach has unique advantages in tuning the pH‐responsiveness of self‐assembled peptides across a large pH range in a complex biological environment. We anticipate the ionizable amino acids developed here can be widely applicable to the synthesis and self‐assembly of many amphiphilic peptides with endowed pH‐responsive properties to enhance their biological activities toward applications ranging from targeted therapeutic delivery to proton transport.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2012

Site-specific incorporation of redox active amino acids into proteins

Compositions and methods of producing components of protein biosynthetic machinery that include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, and orthogonal pairs of tRNAs/synthetases, which incorporate redox active amino acids into proteins are provided. Methods for identifying these orthogonal pairs are also provided along with methods of producing proteins with redox active amino acids using these orthogonal pairs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Site-specific incorporation of redox active amino acids into proteins

Compositions and methods of producing components of protein biosynthetic machinery that include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, and orthogonal pairs of tRNAs/synthetases, which incorporate redox active amino acids into proteins are provided. Methods for identifying these orthogonal pairs are also provided along with methods of producing proteins with redox active amino acids using these orthogonal pairs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2012

Synthesis of amino acid block-copolymer imprinted chiral mesoporous silica and its acoustically-induced optical Kerr effects

Chiral mesoporous SiO{sub 2} (CMS) have been synthesized and studied the Acoustically-Induced Optical Kerr Effects (AIOKE) and the results have been compared with non-chiral mesoporous silica. The CMS with controllable pore sizes (of {approx}3 nm) and high surface areas of ca. 650 m{sup 2}g{sup -1} was synthesized by mimicking the intrinsic chirality of the amino acid block copolymers. The chiral mesoporous materials were characterized through HRTEM, BET, small-angle XRD, {sup 29}Si-NMR and circular dichroism. AIOKE measurements have been performed using an Er:glass 20 ns laser with a 10 Hz frequency repetition. The optimal AIOKE results of the CMS were achieved for 9.7% of the chromophore in the matrices. We found that the AIOKE for the CMS mimicked with chiral block copolymers is quite high compared to the non-chiral SiO{sub 2}. A difference in AIOKE for these two compounds is observed, enabling CMS that can be used for the design of the acoustically-operated quantum electronic devices. - Graphical abstract: Novel chiral mesoporous SiO{sub 2} (CMS) is showing Acoustically-Induced Optical Kerr Effects (AIOKE). Different in AIOKE of two mesoporous materials is observed, enabling CMS can be used for the design of the acoustically-operated quantum electronic devices.Highlights: Black-Right-Pointing-Pointer Chiral mesoporous SiO{sub 2} (CMS) synthesized with amino acid block copolymers. Black-Right-Pointing-Pointer The Acoustically-induced Optical Kerr Effects (AIOKE) of chiral mesoporous SiO{sub 2} studied. Black-Right-Pointing-Pointer AIOKE very high for CMS compared to non chiral SiO{sub 2}. Black-Right-Pointing-Pointer CMS can be used in acoustically-operated quantum electronic devices.

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

Tip-induced domain structures and polarization switching in ferroelectric amino acid glycine

Bioorganic ferroelectrics and piezoelectrics are becoming increasingly important in view of their intrinsic compatibility with biological environment and biofunctionality combined with strong piezoelectric effect and a switchable polarization at room temperature. Here, we study tip-induced domain structures and polarization switching in the smallest amino acid β-glycine, representing a broad class of non-centrosymmetric amino acids. We show that β-glycine is indeed a room-temperature ferroelectric and polarization can be switched by applying a bias to non-polar cuts via a conducting tip of atomic force microscope (AFM). Dynamics of these in-plane domains is studied as a function of an applied voltage and pulse duration. The domain shape is dictated by polarization screening at the domain boundaries and mediated by growth defects. Thermodynamic theory is applied to explain the domain propagation induced by the AFM tip. Our findings suggest that the properties of β-glycine are controlled by the charged domain walls which in turn can be manipulated by an external bias.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2014

Highly efficient inverted organic solar cells using amino acid modified indium tin oxide as cathode

In this paper, we report that highly efficient inverted organic solar cells were achieved by modifying the surface of indium tin oxide (ITO) using an amino acid, Serine (Ser). With the modification of the ITO surface, device efficiency was significantly enhanced from 0.63% to 4.17%, accompanied with an open circuit voltage (Voc) that was enhanced from 0.30 V to 0.55 V. Ultraviolet and X-ray photoelectron spectroscopy studies indicate that the work function reduction induced by the amino acid modification resulting in the decreased barrier height at the ITO/organic interface played a crucial role in the enhanced performances.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Amino acid enantiomers in old and young dissolved organic matter: Implications for a microbial nitrogen pump

Dissolved organic nitrogen (DON) represents the largest reservoir of fixed N in the surface ocean and a significant portion accumulates in the deep sea, where it can persist for millennial time scales. However, like the dissolved organic carbon (DOC) pool, the origin and composition of long-lived, refractory DON remains largely unknown. In recent years, the “microbial carbon pump” hypothesis has emerged from abundant evidence showing that microbial processes are primarily responsible for refractory DOC accumulation. However, a similar mechanism for DON has rarely been investigated. In the study of DON, spectroscopic evidence has indicated a primarily amide composition, implying a dominant contribution from peptides. Therefore, if an analogous “microbial nitrogen pump” controls refractory DON accumulation, the amino acid component should bear increasing signatures of microbial origin with increasing age. Here we investigate the microbial sequestration of N via the production of refractory DON, for the first time considering together DOM Δ 14 C with amino acid (AA) molar abundance (Mol%) and D/L ratio (as a tracer for prokaryotic input). Measurements were made on a unique set of high and low molecular weight (HMW, LMW) DOM isolates with 14 C ages and chemical compositions generally consistent with semi-labile and refractory DOM respectively. The samples were collected in the North Pacific Subtropical Gyre where deep waters contain some of the oldest DOC in the world ocean. We observe higher D/L ratios in older, LMW DOM isolates for almost all analyzed AAs. Using mass spectral data, we also quantify three D-AAs in all samples (D-valine, D-phenylalanine, and D-leucine), which have not previously been confirmed in ocean DOM. These newly identified D-AAs are concentrated in the LMW refractory DOM fraction and have oceanographically consistent depth profiles. Our results suggest that several novel D-AA subgroupings may be unique tracers for different prokaryotic source processes. D-alanine appears to have largely independent cycling from the other D-AAs with a connection to the production of HMW DON, which we hypothesize is linked to water column peptidoglycan. In contrast, D-leucine, D-valine, and D-phenylalanine appear to be most strongly related to the production of LMW DON. Trends in both the HMW and LMW fractions suggest a linkage to sinking particles and local microbial transformations, implying that LMW DON has a direct biological source rather than originating from successive microbial reprocessing of HMW DON. In conclusion, taken together, our observations are consistent with the dominant production of refractory LMW DON by prokaryotic organisms and suggests that different AA sub-groupings that can be used to track different processes within the DON pool.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗