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At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Physiological Adaptations to Progressive Endurance Exercise Training in Adult and Aged Rats: Insights from the Molecular Transducers of Physical Activity Consortium (MoTrPAC)

While regular physical activity is a cornerstone of health, wellness, and vitality, the impact of endurance exercise training on molecular signaling within and across tissues remains to be delineated. The Molecular Transducers of Physical Activity Consortium (MoTrPAC) was established to characterize molecular networks underlying the adaptive response to exercise. Here, we describe the endurance exercise training studies undertaken by the Preclinical Animal Sites Studies component of MoTrPAC, in which we sought to develop and implement a standardized endurance exercise protocol in a large cohort of rats. To this end, Adult (6-mo) and Aged (18-mo) female (n = 151) and male (n = 143) Fischer 344 rats were subjected to progressive treadmill training (5 d/wk, ~70%–75% VO 2 max) for 1, 2, 4, or 8 wk; sedentary rats were studied as the control group. A total of 18 solid tissues, as well as blood, plasma, and feces, were collected to establish a publicly accessible biorepository and for extensive omics-based analyses by MoTrPAC. Treadmill training was highly effective, with robust improvements in skeletal muscle citrate synthase activity in as little as 1–2 wk and improvements in maximum run speed and maximal oxygen uptake by 4–8 wk. For body mass and composition, notable age- and sex-dependent responses were observed. This work in mature, treadmill-trained rats represents the most comprehensive and publicly accessible tissue biorepository, to date, and provides an unprecedented resource for studying temporal-, sex-, and age-specific responses to endurance exercise training in a preclinical rat model.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Molecular Transducers of Physical Activity Consortium (MoTrPAC): Mapping the Dynamic Responses to Exercise

Exercise provides a robust physiological stimulus that evokes cross-talk between a wide range of tissues via hormonal, cellular and molecular signals that when repeated regularly over time (i.e., training) improves physiological capacity, benefits numerous organ systems and decreases the risk for premature mortality. In spite of its fundamental importance, a gap remains in identifying the detailed molecular signals and responses to exercise and its benefits for health and disease prevention. To further knowledge in this emerging area, the Molecular Transducers of Physical Activity Consortium (MoTrPAC) was established to generate a molecular map of the effects of acute and chronic exercise. MoTrPAC investigators are conducting preclinical and clinical studies to better understand the systemic effects of exercise across multiple tissues. The preclinical studies were performed on more than 700 rats with the analysis of twenty or more organs per rat. The clinical study involves a large cohort of ~2600 individuals with a range of ages and fitness levels (untrained, trained, highly trained) who will be evaluated physiologically and by molecular probing of blood, muscle and adipose tissues before and after acute and chronic endurance or resistance exercise. Multi-omic analyses (genomics, epigenomics, transcriptomics, proteomics and metabolomics/lipidomics) will be performed followed by state-of-the-art bioinformatics to create a molecular map of exercise. This mapping project will provide a public database that is expected to enhance our understanding of the health benefits of physical activity in many organ systems and potentially provide insight into mitigating diseases through activity.

Sanford, James A.↗
DOE OSTI2025

Active deep kernel learning of molecular properties from structural embeddings

As vast databases of chemical identities become increasingly available, the challenge shifts to how we effectively explore and leverage these resources to study molecular properties. This paper presents an active learning approach for molecular discovery using deep kernel learning (DKL), demonstrated on the QM9 dataset. DKL links structural embeddings directly to properties, creating organized latent spaces that prioritize relevant property information. By iteratively recalculating embedding vectors in alignment with target properties, DKL uncovers concentrated maxima representing key molecular properties and reveals unexplored regions with potential for innovation. This approach underscores DKL’s potential in advancing molecular research and discovery.

Artificial neural networks↗
DOE OSTI2023

Cryo-EM structures of Uba7 reveal the molecular basis for ISG15 activation and E1-E2 thioester transfer

ISG15 plays a crucial role in the innate immune response and has been well-studied due to its antiviral activity and regulation of signal transduction, apoptosis, and autophagy. ISG15 is a ubiquitin-like protein that is activated by an E1 enzyme (Uba7) and transferred to a cognate E2 enzyme (UBE2L6) to form a UBE2L6-ISG15 intermediate that functions with E3 ligases that catalyze conjugation of ISG15 to target proteins. Despite its biological importance, the molecular basis by which Uba7 catalyzes ISG15 activation and transfer to UBE2L6 is unknown as there is no available structure of Uba7. Here, we present cryo-EM structures of human Uba7 in complex with UBE2L6, ISG15 adenylate, and ISG15 thioester intermediate that are poised for catalysis of Uba7-UBE2L6-ISG15 thioester transfer. Our structures reveal a unique overall architecture of the complex compared to structures from the ubiquitin conjugation pathway, particularly with respect to the location of ISG15 thioester intermediate. Our structures also illuminate the molecular basis for Uba7 activities and for its exquisite specificity for ISG15 and UBE2L6. Altogether, our structural, biochemical, and human cell-based data provide significant insights into the functions of Uba7, UBE2L6, and ISG15 in cells.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

PhenoProfiling: Mapping phenotypic outcomes to molecular determinants of biochemical activity

The aggregate genomes of the trillions of microorganisms within soil, animal hosts, and aquatic systems encode for an extensive functional capacity for myriad biochemical activities. C, N, P, and S metabolism, synthesis of signaling molecules and vitamins, mineralization, and other activities are essential to microbe, community, and plant physiology, and more broadly to climate, water, animal, flora, and human health. The current understanding of the molecular basis for the function of microbial communities stems primarily from comparative metagenomic and metatranscriptomic studies. These same tools are employed to ascertain the impacts to the community resulting from perturbations, such as climate change, emerging pollutants, fires, and seawater infiltration for environmental communities, and dietary changes, xenobiotic exposure, and various disease states for the human gut microbiome. Such studies can identify the potential for a specific function, but they cannot determine that a particular cell is functionally active, nor can they determine the molecular architecture required for function. In short, genes and transcripts alone fail to reveal the complex subcellular arrangement of proteins and molecules that elicit a given phenotype in a microbial cell.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

In situ x-ray absorption investigations of a heterogenized molecular catalyst and its interaction with a carbon nanotube support

A highly active heterogenized molecular CO 2 reduction catalyst on a conductive carbon support is investigated to identify if its improved catalytic activity can be attributed to strong electronic interactions between catalyst and support. The molecular structure and electronic character of a [Re +1 (tBu-bpy)(CO) 3 Cl] (tBu-bpy = 4,4'-tert-butyl-2,2'-bipyridine) catalyst deposited on multiwalled carbon nanotubes are characterized using Re L 3 -edge x-ray absorption spectroscopy under electrochemical conditions and compared to the homogeneous catalyst. The Re oxidation state is characterized from the near-edge absorption region, while structural changes of the catalyst are assessed from the extended x-ray absorption fine structure under reducing conditions. Chloride ligand dissociation and a Re-centered reduction are both observed under applied reducing potential. The results confirm weak coupling of [Re(tBu-bpy)(CO) 3 Cl] with the support, since the supported catalyst exhibits the same oxidation changes as the homogeneous case. However, these results do not preclude strong interactions between a reduced catalyst intermediate and the support, preliminarily investigated here using quantum mechanical calculations. Thus, our results suggest that complicated linkage schemes and strong electronic interactions with the initial catalyst species are not required to improve the activity of heterogenized molecular catalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Molecular understanding of heteronuclear active sites in heme–copper oxidases, nitric oxide reductases, and sulfite reductases through biomimetic modelling

Heme-copper oxidases (HCO), nitric oxide reductases (NOR), and sulfite reductases (SiR) catalyze the multi-electron and multi-proton reductions of O 2 , NO, and SO 3 2- , respectively. Each of these reactions is important to drive cellular energy production through respiratory metabolism and HCO, NOR, and SiR evolved to contain heteronuclear active sites containing heme/copper, heme/nonheme iron, and heme-[4Fe-4S] centers, respectively. The complexity of the structures and reactions of these native enzymes, along with their large sizes and/or membrane associations, make it challenging to fully understand the crucial structural features responsible for the catalytic properties of these active sites. Here, we summarize progress that has been made to better understand these heteronuclear metalloenzymes at the molecular level though study of the native enzymes along with insights gained from biomimetic models comprising either small molecules or proteins. Further understanding the reaction selectivity of these enzymes is discussed through comparisons of their similar heteronuclear active sites, and we offer outlook for further investigations and areas of ongoing study.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Molecular basis for antiviral activity of two pediatric neutralizing antibodies targeting SARS-CoV-2 Spike RBD

Neutralizing antibodies (NAbs) hold great promise for clinical interventions against SARS-CoV-2 variants of concern (VOCs). Understanding NAb epitopedependent antiviral mechanisms is crucial for developing vaccines and therapeutics against VOCs. Here we characterized two potent NAbs, EH3 and EH8, isolated from an unvaccinated pediatric patient with exceptional plasma neutralization activity. EH3 and EH8 cross-neutralize the early VOCsandmediatestrong Fc-dependent effector activity in vitro. Structural analyses of EH3 and EH8 in complex with the receptor-binding domain (RBD) revealed the molecular determinantsoftheepitope-drivenprotectionandVOCevasion.WhileEH3represents the prevalent IGHV3-53 NAb whose epitope substantially overlaps with the ACE2 binding site, EH8 recognizes a narrow epitope exposed in both RBD-up and RBD-down conformations. When tested in vivo, a single-dose prophylactic administration of EH3 fully protected stringent K18-hACE2 micefrom lethal challenge with Delta VOC. Our study demonstrates that protective NAbs responses converge in pediatric and adult SARS-CoV-2 patients.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

A Molecular View of Methane Activation on Ni(111) through Enhanced Sampling and Machine Learning

A combination of machine learned interatomic potentials (MLIPs) and enhanced sampling simulations is used to investigate the activation of methane on a Ni(111) surface. The work entails the development and iterative refinement of MLIPs, initially trained on a dataset constructed via ab initio molecular dynamics (AIMD) simulations, supplemented by adaptive biasing forces, to enrich the sampling of catalytically relevant configurations. Our results reveal that by incorporating collective variables that capture the behavior of the reactant molecule, as well as additional frames that describe the dynamic response of the catalytic surface, it is possible to enhance considerably the accuracy of predicted energies and forces. By employing enhanced sampling schemes in the refinement of the MLIP, we systematically explore the potential energy surface, leading to a refined MLIP capable of predicting DFT-level energies and forces and replicating key geometric characteristics of the catalytic system. The resulting free energy landscapes at several temperatures provide a detailed view of the thermodynamics and dynamics of methane activation. Specifically, as methane approaches and dissociates on the catalytic surface, the process involves the dynamic interplay of CH 4 and the Ni catalyst that includes both enthalpic and entropic contributions. The progression towards the transition state involves an CH 4 moiety that is increasingly restrained in its ability to rotate or translate, while the stage following the transition state is characterized by a notable rise of the Ni atom that interacts with the cleaved C–H bond. Furthermore, this leads to an increase in the mobility of the adsorbed species, a feature that becomes more pronounced at higher temperatures.

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

Structural analysis of the NifL-NifA complex reveals the molecular basis of anti-activation of nitrogen fixation gene expression in Azotobacter vinelandii

Understanding the molecular basis of regulated nitrogen (N 2 ) fixation is essential for engineering N 2 -fixing bacteria that fulfill the demand of crop plants for fixed nitrogen, reducing our reliance on synthetic nitrogen fertilizers. In Azotobacter vinelandii and many other members of Proteobacteria, the two-component system comprising the anti-activator protein (NifL) and the Nif-specific transcriptional activator (NifA)controls the expression of nif genes, encoding the nitrogen fixation machinery. The NifL-NifA system evolved the ability to integrate several environmental cues, such as oxygen, nitrogen, and carbon availability. The nitrogen fixation machinery is thereby only activated under strictly favorable conditions, enabling diazotrophs to thrive in competitive environments. While genetic and biochemical studies have enlightened our understanding of how NifL represses NifA, the molecular basis of NifA sequestration by NifL depends on structural information on their interaction. Here, we present mechanistic insights into how nitrogen fixation is regulated by combining biochemical and genetic approaches with a low-resolution cryo-electron microscopy (cryo-EM) map of the oxidized NifL-NifA complex. Our findings define the interaction surface between NifL and NifA and reveal how this interaction can be manipulated to generate bacterial strains with increased nitrogen fixation rates able to secrete surplus nitrogen outside the cell, a crucial step in engineering improved nitrogen delivery to crop plants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Design, synthesis, molecular docking, antimicrobial, and antioxidant activities of new phenylsulfamoyl carboxylic acids of pharmacological interest

Abstracts: The research explores the facile synthesis of some new phenylsulfamoyl carboxylic acids, their molecular docking, antimicrobial, and antioxidant activities. The procedure involved the mild reaction of amino acids with benzenesulfonyl chloride in a medium of aqueous base. The compounds were characterized using FTIR, {sup 1}H-NMR, {sup 13}C-NMR, and an elemental analysis. They were tested for their antimicrobial activities against Staphylococcus aureus, Escherichia coli, Bacillus subtilis, Pseudomonas aeruginosa, Salmonella typhi, Candida albicans, and Aspergillus niger microorganisms. The antioxidant activity of the compounds were measured in vitro by the inhibition of generated stable 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical. The molecular docking was carried out properly and five different disease conditions were studied, namely: trypanosomiasis, malaria, bacterial, fungal infections, and oxidative stress. From the results, compounds 4c, 4d, 4e, and 4g possess more excellent in vitro antibacterial and antifungal activities than the standard drug Ofloxacin used. Compound 4e displayed the most excellent antioxidant activity. Compound 4g showed significant 2D interaction with amino acid residue of urate oxidase from Aspergillus flavus complexed with uracil. Interestingly, compounds 4a, 4c, 4d, 4e, and 4g exhibited excellent antibacterial, antifungal, antioxidant, antitrypanosome, and antimalaria activities comparable to the corresponding standard drugs such as Penicillin, Ketoconazole; α-Tocopherol, Melarsoprol, and Chloroquine respectively. All the compounds were confirmed drug-like according to “Lipinski’s rule of five”. The compounds were found to be promising antibacterial, antifungal, antioxidant, and antitrypanosome agents.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Realization of an Asymmetric Non‐Aqueous Redox Flow Battery through Molecular Design to Minimize Active Species Crossover and Decomposition

Abstract This communication presents a mechanism‐based approach to identify organic electrolytes for non‐aqueous redox flow batteries (RFBs). Symmetrical flow cell cycling of a pyridinium anolyte and a cyclopropenium catholyte resulted in extensive capacity fade due to competing decomposition of the pyridinium species. Characterization of this decomposition pathway enabled the rational design of next‐generation anolyte/catholyte pairs with dramatically enhanced cycling performance. Three factors were identified as critical for slowing capacity fade: (1) separating the anolyte–catholyte in an asymmetric flow cell using an anion exchange membrane (AEM); (2) moving from monomeric to oligomeric electrolytes to limit crossover through the AEM; and (3) removing the basic carbonyl moiety from the anolyte to slow the protonation‐induced decomposition pathway. Ultimately, these modifications led to a novel anolyte–catholyte pair that can be cycled in an AEM‐separated asymmetric RFB for 96 h with >95 % capacity retention at an open circuit voltage of 1.57 V.

Shrestha, Anuska↗
DOE OSTI2024

Structure and Interactions of HIV-1 gp41 CHR-NHR Reverse Hairpin Constructs Reveal Molecular Determinants of Antiviral Activity

Engineered reverse hairpin constructs containing a partial C-heptad repeat (CHR) sequence followed by a short loop and full-length N-heptad repeat (NHR) were previously shown to form trimers in solution and to be nanomolar inhibitors of HIV-1 Env mediated fusion. Their target is the in situ gp41 fusion intermediate, and they have similar potency to other previously reported NHR trimers. However, their design implies that the NHR is partially covered by CHR, which would be expected to limit potency. An exposed hydrophobic pocket in the folded structure may be sufficient to confer the observed potency, or they may exist in a partially unfolded state exposing full length NHR. Here, in this study, we examined their structure by crystallography, CD and fluorescence, establishing that the proteins are folded hairpins both in crystal form and in solution. We examined unfolding in the milieu of the fusion reaction by conducting experiments in the presence of a membrane mimetic solvent and by engineering a disulfide bond into the structure to prevent partial unfolding. We further examined the role of the hydrophobic pocket, using a hairpin-small molecule adduct that occluded the pocket, as confirmed by X-ray footprinting. The results demonstrated that the NHR region nominally covered by CHR in the engineered constructs and the hydrophobic pocket region that is exposed by design were both essential for nanomolar potency and that interaction with membrane is likely to play a role in promoting the required inhibitor structure. The design concepts can be applied to other Class 1 viral fusion proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

The Molecular Path Approaching the Active Site in Catalytic Metal–Organic Frameworks

How molecules approach, bind at, and release from catalytic sites is key to heterogeneous catalysis, including for emerging metal-organic framework (MOF)-based catalysts. Here, we use in situ synchrotron X-ray scattering analysis to evaluate the dominant binding sites for reagent and product molecules in the vicinity of catalytic Ni-oxo clusters in NU-1000 with different surface functionalization under conditions approaching those used in catalysis. The locations of the reagent and product molecules within the pores can be linked to the activity for ethylene hydrogenation. For the most active catalyst, ethylene reagent molecules bind close to the catalytic clusters, but only at temperatures approaching experimentally observed onset of catalysis. The ethane product molecules favor a different binding location suggesting that the product is readily released from the active site. An unusual guest-dependence of the framework negative thermal expansion is documented. We hypothesize that reagent and product binding sites reflect the pathway through the MOF to the active site and can be used to identify key factors that impact the catalytic activity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗