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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 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Electronic Interactions Between the Receptor-Binding Domain of Omicron Variants and Angiotensin-Converting Enzyme 2: A Novel Amino Acid–Amino Acid Bond Pair Concept

SARS-CoV-2 remains a severe threat to worldwide public health, particularly as the virus continues to evolve and diversify into variants of concern (VOCs). Among these VOCs, Omicron variants exhibit unique phenotypic traits, such as immune evasion, transmissibility, and severity, due to numerous spike protein mutations and the rapid subvariant evolution. These Omicron subvariants have more than 15 mutations in the receptor-binding domain (RBD), a region of the SARS-CoV-2 spike protein that is important for recognition and binding with the angiotensin-converting enzyme 2 (ACE2) human receptor. To address the impact of these high numbers of Omicron mutations on the binding process, we have developed a novel method to precisely quantify amino acid interactions via the amino acid–amino acid bond pair (AABP). We applied this concept to investigate the interface interactions of the RBD–ACE2 complex in four Omicron Variants (BA.1, BA.2, BA.5, and XBB.1.16) with its Wild Type counterpart. Based on the AABP analysis, we have identified all the sites that are affected by mutation and have provided evidence that unmutated sites are also impacted by mutation. We have calculated that the binding between RBD and ACE2 is strongest in OV BA.1, followed by OV BA.2, WT, OV BA.5, and OV XBB.1.16. We also present the partial charge values for all 311 residues across these five models. Our analysis provides a detailed understanding of changes caused by mutation in each Omicron interface complex.

Biochemistry & Molecular Biology↗
DOE OSTI2019

Total Protein Analysis in Algae via Bulk Amino Acid Detection: Optimization of Amino Acid Derivatization after Hydrolysis with O -Phthalaldehyde 3-Mercaptopropionic Acid (OPA-3MPA)

The analysis of protein in algal biomass is one of the most critical areas of commercial development of algae characterization for nutritional or other high value applications. A new rapid and accurate method is required that can be widely implemented and that is free from interferences from the complex algal biomass matrix. We developed a simple spectrophotometric method for primary amino acid quantification bulk measurement in an acid hydrolyzed algal biomass preparation, as an alternative to the more labor-intensive amino HPLC acid analysis or less specific nitrogen-to-protein conversion. We have validated an O -phthalaldehyde (OPA)-based derivatization method, showing accurate and linear quantification for standard reference amino acids as well as mixtures, mimicking the amino acid complexity found in algal biomass. The presence of interferences that may be derived from the complex biomass biochemical composition was tested during the method validation phase. We document the application of a novel method of OPA derivatization with 3-mercaptopropionic acid (3MPA) to determine the total amino acid content of harvested algal biomass collected from different, controlled cultivation conditions and demonstrated a within 10% accuracy against a reference measurement of amino acid content in at least 4 species and 10 algal biomass samples, across early, mid, and late-stages of cultivation.

09 BIOMASS FUELS↗
DOE OSTI2021

Carbon dioxide capture with aqueous amino acids: Mechanistic study of amino acid regeneration by guanidine crystallization and process intensification

CO 2 capture from powerplant-generated flue gas via a phase-changing process involving absorption with aqueous amino acids (e.g., glycine or sarcosine) and bicarbonate crystallization with bis-iminoguanidines (e.g., glyoxal-bis-iminoguanidine or GBIG) is investigated in this paper. This process is of high interest due to its potential to decrease the energy penalty for CO 2 capture by significantly reducing the solvent regeneration energy typically associated with aqueous amine solvents. A critical step in the proposed CO 2 capture mechanism is the regeneration of the amino acid by removal of protons and bicarbonate ions from solution through crystallization of GBIGH 2 2+ bicarbonate salt. Here, we investigated the thermodynamics and kinetics of glycine regeneration by crystallization of GBIGH 2 2+ (HCO 3 – ) 2 (H 2 O) 2 . A theoretical model was developed and compared to experimental data to simulate and predict the glycine regeneration and determine its reaction mechanism. This combined experimental and theoretical study led to the conclusion that, while the GBIGH 2 2+ bicarbonate crystallization step provides most of the thermodynamic driving force for the glycine regeneration, the rate-limiting step is the protonation of GBIG prior to crystallization. The CO 2 loading and amino acid regeneration steps were combined into a single, intensified process using a bubble column reactor. The CO 2 loading capacity of GBIG was experimentally determined to be roughly 1.36 mol CO 2 per mol GBIG. These results provide the fundamental basis for developing an effective carbon capture technology with phase-changing amino acid/guanidine absorbents.

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

Electronic coupling through natural amino acids

Myriad scientific domains concern themselves with biological electron transfer (ET) events that span across vast scales of rate and efficiency through a remarkably fine-tuned integration of amino acid (AA) sequences, electronic structure, dynamics, and environment interactions. Within this intricate scheme, many questions persist as to how proteins modulate electron-tunneling properties. To help elucidate these principles, we develop a model set of peptides representing the common α-helix and β-strand motifs including all natural AAs within implicit protein-environment solvation. Using an effective Hamiltonian strategy with density functional theory, we characterize the electronic coupling through these peptides, furthermore considering side-chain dynamics. For both motifs, predictions consistently show that backbone-mediated electronic coupling is distinctly sensitive to AA type (aliphatic, polar, aromatic, negatively charged and positively charged), and to side-chain orientation. The unique properties of these residues may be employed to design activated, deactivated, or switch-like superexchange pathways. Electronic structure calculations and Green’s function analyses indicate that localized shifts in the electron density along the peptide play a role in modulating these pathways, and further substantiate the experimentally observed behavior of proline residues as superbridges. The distinct sensitivities of tunneling pathways to sequence and conformation revealed in this electronic coupling database help improve our fundamental understanding of the broad diversity of ET reactivity and provide guiding principles for peptide design.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

phosaa14SB and phosaa19SB: Updated Amber Force Field Parameters for Phosphorylated Amino Acids

Phosphorylated amino acids are involved in many cell regulatory networks; proteins containing these post-translational modifications are widely studied both experimentally and computationally. Simulations are used to investigate a wide range of structural and dynamic properties of biomolecules, such as ligand binding, enzyme-reaction mechanisms, and protein folding. However, the development of force field parameters for the simulation of proteins containing phosphorylated amino acids using the Amber program has not kept pace with the development of parameters for standard amino acids, and it is challenging to model these modified amino acids with accuracy comparable to proteins containing only standard amino acids. In particular, the popular ff14SB and ff19SB models do not contain parameters for phosphorylated amino acids. Here, the dihedral parameters for the side chains of the most common phosphorylated amino acids are trained against reference data from QM calculations adopting the ff14SB approach, followed by validation against experimental data. Finally, library files and corresponding parameter files are provided, with versions that are compatible with both ff14SB and ff19SB.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2017

Evaluating the role of acidic, basic, and polar amino acids and dipeptides on a molecular electrocatalyst for H 2 oxidation

Amino acids and peptides have been shown to have a significant influence on the H2 production and oxidation reactivity of Ni(P R 2 N R’ 2 ) 2 , where P R 2 N R’ 2 = 1,5-diaza-3,7-diphosphacyclooctane, R is either phenyl (Ph) or cyclohexyl (Cy), and R’ is either an amino acid or peptide. Most recently, the Ni(P Cy 2 Naminoacid 2 ) 2 complexes (CyAA) have shown enhanced H 2 oxidation rates, water solubility, and in the case of arginine (CyArg) and phenylalanine (CyPhe), electrocatalytic reversibility. Both the backbone –COOH and side chain interactions were shown to be critical to catalytic performance. Here we further investigate the roles of the outer coordination sphere by evaluating amino acids with acidic, basic, and hydrophilic side chains, as well as dipeptides which combine multiple successful features from previous complexes. Six new complexes were prepared, three containing single amino acids: aspartic acid (CyAsp), lysine (CyLys), and serine (CySer) and three containing dipeptides: glycine-phenylalanine (Cy(GlyPhe)), phenylalanine-glycine (Cy(PheGly)), and aspartic acid-phenylananine (Cy(AspPhe)). The resulting catalytic performance demonstrates that complexes need both interactions between side chain and –COOH groups for fast, efficient catalysis. The fastest of all of the catalysts, Cy(AspPhe), had both of these features, while the other dipeptide complexes with an amide replacing the -COOH were both slower; however, the amide group was demonstrated to participate in the proton pathway when side chain interactions are present to position it. Both the hydrophilic and basic side chains, notably lacking in side chain interactions, significantly increased the overpotential, with only modest increases in TOF. Of all of the complexes, only CyAsp was reversible at room temperature, and only in water, the first of these complexes to demonstrate room temperature reversibility in water. These results continue to provide and solidify design rules for controlling reactivity and efficiency of Ni(P 2 N 2 ) 2 complexes with the outer coordination sphere.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Distinguishing enantiomeric amino acids with chiral cyclodextrin adducts and structures for lossless ion manipulations

Enantiomeric molecular evaluations remain an enormous challenge for current analytical techniques. To date, derivatizations strategies and long separation times are generally required in these studies, and the development and implementation of new approaches is greatly desired to increase speed and distinguish currently unresolvable compounds. Herein, we describe a method using chiral cyclodextrin adducts and structures for lossless ion manipulations (SLIM) ion mobility to achieve rapid, high resolution separations of D and L enantiomeric amino acids. In the analyses, chiral cyclodextrin adducts are added to each sample. Two cyclodextrins were found to sandwich each amino acid and form host-guest noncovalent complexes that were distinct for each D and L amino acid pair studied and thus separable with ion mobility (IM) in SLIM devices. The SLIM was also used to accumulate much larger ion populations than previously feasible for evaluation and therefore allow enantiomeric measurements of higher sensitivity and resolution than previously reported by any other IM-based approach.

chiral separations, cyclodextrins, enantiomers, io↗
DOE OSTI2026

Contrasting effects of glutamate and branched-chain amino acid metabolism on acid tolerance in a Castellaniella isolate from acidic groundwater

Groundwater acidification co-occurring with nitrate pollution is a common, global environmental health hazard. Denitrifying bacteria have been leveraged for the in situ removal of nitrate in groundwater. However, co-existing stressors—such as low pH—reduce the efficacy of biological removal processes. Castellaniella sp. str. MT123 is a complete denitrifier that was isolated from acidic, nitrate-contaminated groundwater. The strain grows robustly by nitrate respiration at pH < 6.0, completely reducing nitrate to dinitrogen gas. Genomic analyses of MT123 revealed few previously characterized acid tolerance genes. Thus, we utilized a combination of proteomics, metabolomics, and competitive mutant fitness to characterize the genetic mechanisms of MT123 acclimation to growth under mildly acidic conditions. We found that glutamate accumulation is critical in the acid acclimation of MT123, possibly through consumption of intracellular protons via glutamate decarboxylation to GABA. This is despite the fact that MT123 lacks the canonical glutamate decarboxylase-glutamate/GABA antiporter system implicated in acid tolerance in other bacteria. In contrast, branched-chain amino acid (BCAA) accumulation was detrimental to cell growth at lower pHs, possibly through indirect mechanisms impacting the cellular glutamate pool. Genetic analysis previously linked MT123 to a population of Castellaniella that bloomed—concurrent to nitrate removal—during a biostimulation effort to reduce groundwater nitrate concentrations at MT123’s location of origin. Thus, our analyses provide novel insight into mechanisms of acclimation to acidic conditions in a strain with significant potential for nitrate bioremediation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Potential Foldamers Based on an ortho- Terphenyl Amino Acid

We describe the synthesis and characterization of a new class of oligomers built from a terphenyl-based amino acid. Here, these oligomeric amides are of interest because the adoption of specific conformations could potentially be driven by the coordinated formation of inter-residue hydrogen bonds and aromatic interactions. Although high-resolution structural data have proven inaccessible, circular dichroism and nuclear magnetic resonance studies suggest that the new oligomers fold concomitantly with discrete self-association in chloroform. Molecular simulations find no sign of folding as a monomer, and in fact suggest that hydrogen bond patterning is anti-cooperative, inhibiting longer helices.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Structural basis of amino acid surveillance by higher-order tRNA-mRNA interactions

Amino acid availability in Gram-positive bacteria is monitored by T-box riboswitches. T-boxes directly bind tRNAs, assess their aminoacylation state, and regulate the transcription or translation of downstream genes to maintain nutritional homeostasis. Here in this paper, we report cocrystal and cryo-EM structures of Geobacillus kaustophilus and Bacillus subtilis T-box–tRNA complexes, detailing their multivalent, exquisitely selective interactions. The T-box forms a U-shaped molecular vise that clamps the tRNA, captures its 3' end using an elaborate ‘discriminator’ structure, and interrogates its aminoacylation state using a steric filter fashioned from a wobble base pair. In the absence of aminoacylation, T-boxes clutch tRNAs and form a continuously stacked central spine, permitting transcriptional readthrough or translation initiation. A modeled aminoacyl disrupts tRNA-T-box stacking, severing the central spine and blocking gene expression. Our data establish a universal mechanism of amino acid sensing on tRNAs and gene regulation by T-box riboswitches and exemplify how higher-order RNA-RNA interactions achieve multivalency and specificity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Electron Spin-Polarization Dependent Damage to Chiral Amino Acid l-Histidine

The damage of approximately monolayer films of L-histidine by low-energy spin-polarized electrons (SPE) ejected from a magnetized cobalt substrate has been probed using X-ray photoelectron spectroscopy (XPS). Average damage cross sections for N-containing motifs of L-histidine are 25-30 and 2-5 Mb for zwitterions and neutral molecules, respectively. Here, the magnetization direction of the substrate, which controls the ejected SPE helicity, was reversed in situ, and statistically significant differences in the damage cross sections of 10-30% were measured between positive and negative electron helicities. This is the first measurement of spin dichroism (SD) in an amino acid. The differential cross sections suggest that inelastic scattering of SPE with chiral molecules could contribute to the persistence of one enantiomer vs the other under certain irradiation conditions, particularly for the zwitterionic species.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Cryo-EM structure of the human neutral amino acid transporter ASCT2

Human ASCT2 belongs to the SLC1 family of secondary transporters and is specific for the transport of small neutral amino acids. ASCT2 is upregulated in cancer cells and serves as the receptor for many retroviruses; hence, it has importance as a potential drug target. Here we used single-particle cryo-EM to determine a structure of the functional and unmodified human ASCT2 at 3.85-Å resolution. ASCT2 forms a homotrimeric complex in which each subunit contains a transport and a scaffold domain. Prominent extracellular extensions on the scaffold domain form the predicted docking site for retroviruses. Relative to structures of other SLC1 members, ASCT2 is in the most extreme inward-oriented state, with the transport domain largely detached from the central scaffold domain on the cytoplasmic side. In conclusion, this domain detachment may be required for substrate binding and release on the intracellular side of the membrane.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Tri-peptide reference structures for the calculation of relative solvent accessible surface area in protein amino acid residues

Relative amino acid residue solvent accessibility values allow the quantitative comparison of atomic solvent-accessible surface areas in different residue types and physical environments in proteins and in protein structural alignments. Geometry-optimised tri-peptide structures in extended solvent-exposed reference conformations have been obtained for 43 amino acid residue types at a high level of quantum chemical theory. Significant increases in side-chain solvent accessibility, offset by reductions in main-chain atom solvent exposure, were observed for standard residue types in partially geometry-optimised structures when compared to non-minimised models built from identical sets of proper dihedral angles abstracted from the literature. Optimisation of proper dihedral angles led most notably to marked increases of up to 54% in proline main-chain atom solvent accessibility compared to literature values. Similar effects were observed for fully-optimised tri-peptides in implicit solvent. The relief of internal strain energy was associated with systematic variation in N, C α and C β atom solvent accessibility across all standard residue types. The results underline the importance of optimisation of ‘hard’ degrees of freedom (bond lengths and valence bond angles) and improper dihedral angle values from force field or other context-independent reference values, and impact on the use of standardised fixed internal co-ordinate geometry in sampling approaches to the determination of absolute values of protein amino acid residue solvent accessibility. Finally, quantum chemical methods provide a useful and accurate alternative to molecular mechanics methods to perform energy minimisation of peptides containing non-standard (chemically modified) amino acid residues frequently present in experimental protein structure data sets, for which force field parameters may not be available. Reference tri-peptide atomic co-ordinate sets including hydrogen atoms are made freely available.

59 BASIC BIOLOGICAL SCIENCES↗