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At least 217 records · Page 12

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DOE OSTI2025

Defining the Antitumor Mechanism of Action of a Clinical-stage Compound as a Selective Degrader of the Nuclear Pore Complex

Cancer cells are acutely dependent on nuclear transport due to elevated transcriptional activity, suggesting an unrealized opportunity for selective therapeutic inhibition of the nuclear pore complex (NPC). Through large-scale phenotypic profiling of cancer cell lines, genome-scale functional genomic modifier screens, and mass spectrometry–based proteomics, we discovered that the clinical drug PRLX-93936 is a molecular glue that binds and reprograms the TRIM21 ubiquitin ligase to degrade the NPC. Upon compound-induced TRIM21 recruitment, the nuclear pore is ubiquitylated and degraded, resulting in the loss of short-lived cytoplasmic mRNA transcripts and the induction of cancer cell apoptosis. Direct compound binding to TRIM21 was confirmed via surface plasmon resonance and X-ray crystallography, whereas compound-induced TRIM21–nucleoporin complex formation was demonstrated through multiple orthogonal approaches in cells and in vitro. Phenotype-guided optimization yielded compounds with 10-fold greater potency and drug-like properties, along with robust pharmacokinetics and efficacy against pancreatic cancer xenografts and patient-derived organoids.

Yuan, Linjie [Stanford School of Medicine, CA (Uni↗

DOE OSTI2022

Characterization of Heparin’s Conformational Ensemble by Molecular Dynamics Simulations and Nuclear Magnetic Resonance Spectroscopy

Heparin is a highly charged, polysulfated polysaccharide and serves as an anticoagulant. Heparin binds to multiple proteins throughout the body, suggesting a large range of potential therapeutic applications. Although its function has been characterized in multiple physiological contexts, heparin’s solution conformational dynamics and structure–function relationships are not fully understood. Molecular dynamics (MD) simulations facilitate the analysis of a molecule’s underlying conformational ensemble, which then provides important information necessary for understanding structure–function relationships. However, for MD simulations to afford meaningful results, they must both provide adequate sampling and accurately represent the energy properties of a molecule. The aim of this study is to compare heparin’s conformational ensemble using two well-developed force fields for carbohydrates, known as GLYCAM06 and CHARMM36, using replica exchange molecular dynamics (REMD) simulations, and to validate these results with NMR experiments. In this work, the anticoagulant sequence, an ultra-low-molecular-weight heparin, known as Arixtra (fondaparinux, sodium), was simulated with both parameter sets. The results suggest that GLYCAM06 matches experimental nuclear magnetic resonance three-bond J-coupling values measured for Arixtra better than CHARMM36. In addition, NOESY and ROESY experiments suggest that Arixtra is very flexible in the sub-millisecond time scale and does not adopt a unique structure at 25 C. Moreover, GLYCAM06 affords a much more dynamic conformational ensemble for Arixtra than CHARMM36.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

A phage nucleus-associated RNA-binding protein is required for jumbo phage infection

Abstract Large-genome bacteriophages (jumbo phages) of the proposed family Chimalliviridae assemble a nucleus-like compartment bounded by a protein shell that protects the replicating phage genome from host-encoded restriction enzymes and DNA-targeting CRISPR-Cas nucleases. While the nuclear shell provides broad protection against host nucleases, it necessitates transport of mRNA out of the nucleus-like compartment for translation by host ribosomes, and transport of specific proteins into the nucleus-like compartment to support DNA replication and mRNA transcription. Here, we identify a conserved phage nuclear shell-associated protein that we term Chimallin C (ChmC), which adopts a nucleic acid-binding fold, binds RNA with high affinity in vitro, and binds phage mRNAs in infected cells. ChmC also forms phase-separated condensates with RNA in vitro. Targeted knockdown of ChmC using mRNA-targeting dCas13d results in accumulation of phage-encoded mRNAs in the phage nucleus, reduces phage protein production, and compromises virion assembly. Taken together, our data show that the conserved ChmC protein plays crucial roles in the viral life cycle, potentially by facilitating phage mRNA translocation through the nuclear shell to promote protein production and virion development.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Spatial Engineering Direct Cooperativity between Binding Sites for Uranium Sequestration

Preorganization is a basic design principle used by nature that allows for synergistic pathways to be expressed. Herein, a full account of the conceptual and experimental development from randomly distributed functionalities to a convergent arrangement that facilitates cooperative binding is given, thus conferring exceptional affinity toward the analyte of interest. The resulting material with chelating groups populated adjacently in a spatially locked manner displays up to two orders of magnitude improvement compared to a random and isolated manner using uranium sequestration as a model application. This adsorbent shows exceptional extraction efficiencies, capable of reducing the uranium concentration from 5 ppm to less than 1 ppb within 10 min, even though the system is permeated with high concentrations of competing ions. The efficiency is further supported by its ability to extract uranium from seawater with an uptake capability of 5.01 mg g -1 , placing it among the highest-capacity seawater uranium extraction materials described to date. The concept presented here uncovers a new paradigm in the design of efficient sorbent materials by manipulating the spatial distribution to amplify the cooperation of functions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2020

Quantified limits of the nuclear landscape

The chart of the nuclides is limited by particle drip lines beyond which nuclear stability to proton or neutron emission is lost. Predicting the range of particle-bound isotopes poses an appreciable challenge for nuclear theory as it involves extreme extrapolations of nuclear masses well beyond the regions where experimental information is available. Still, quantified extrapolations are crucial for a wide variety of applications, including the modeling of stellar nucleosynthesis. We use microscopic nuclear global mass models, current mass data, and Bayesian methodology to provide quantified predictions of proton and neutron separation energies as well as Bayesian probabilities of existence throughout the nuclear landscape all the way to the particle drip lines. Here, we apply nuclear density functional theory with several energy density functionals. We also consider two global mass models often used in astrophysical nucleosynthesis simulations. To account for uncertainties, Bayesian Gaussian processes are trained on the separation-energy residuals for each individual model, and the resulting predictions are combined via Bayesian model averaging. This framework allows to account for systematic and statistical uncertainties and propagate them to extrapolative predictions. We establish and characterize the drip-line regions where the probability that the nucleus is particle- bound decreases from 1 to 0. In these regions, we provide quantified predictions for one- and two-nucleon separation energies. According to our Bayesian model averaging analysis, 7759 nuclei with Z ≤ 119 have a probability of existence ≥ 0.5. The extrapolation results obtained in this study will be put through stringent tests when new experimental information on existence and masses of exotic nuclei becomes available. In this respect, the quantified landscape of nuclear existence obtained in this study should be viewed as a dynamical prediction that will be fine-tuned when new experimental information and improved global mass models become available.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Structural and biochemical analyses of the nuclear IκBζ protein in complex with the NF-κB p50 homodimer

As part of the efforts to understand nuclear IκB function in NF-κB-dependent gene expression, we report an X-ray crystal structure of the IκBζ ankyrin repeat domain in complex with the dimerization domain of the NF-κB p50 homodimer. IκBζ possesses an N-terminal α helix that conveys domain folding stability. Affinity and specificity of the complex depend on a small portion of p50 at the nuclear localization signal. The model suggests that only one p50 subunit supports binding with IκBζ, and biochemical experiments confirm that IκBζ associates with DNA-bound NF-κB p50:RelA heterodimers. Comparisons of IκBζ:p50 and p50:κB DNA complex crystallographic models indicate that structural rearrangement is necessary for ternary complex formation of IκBζ and p50 with DNA.

Cell Biology↗

NASA NTRS2000

Cardiac tissue enriched factors serum response factor and GATA-4 are mutual coregulators

Combinatorial interaction among cardiac tissue-restricted enriched transcription factors may facilitate the expression of cardiac tissue-restricted genes. Here we show that the MADS box factor serum response factor (SRF) cooperates with the zinc finger protein GATA-4 to synergistically activate numerous myogenic and nonmyogenic serum response element (SRE)-dependent promoters in CV1 fibroblasts. In the absence of GATA binding sites, synergistic activation depends on binding of SRF to the proximal CArG box sequence in the cardiac and skeletal alpha-actin promoter. GATA-4's C-terminal activation domain is obligatory for synergistic coactivation with SRF, and its N-terminal domain and first zinc finger are inhibitory. SRF and GATA-4 physically associate both in vivo and in vitro through their MADS box and the second zinc finger domains as determined by protein A pullout assays and by in vivo one-hybrid transfection assays using Gal4 fusion proteins. Other cardiovascular tissue-restricted GATA factors, such as GATA-5 and GATA-6, were equivalent to GATA-4 in coactivating SRE-dependent targets. Thus, interaction between the MADS box and C4 zinc finger proteins, a novel regulatory paradigm, mediates activation of SRF-dependent gene expression.

NASA Discipline Musculoskeletal↗

NASA NTRS2000

Skeletal muscle Ca(2+)-independent kinase activity increases during either hypertrophy or running

Spikes in free Ca(2+) initiate contractions in skeletal muscle cells, but whether and how they might signal to transcription factors in skeletal muscles of living animals is unknown. Since previous studies in non-muscle cells have shown that serum response factor (SRF) protein, a transcription factor, is phosphorylated rapidly by Ca(2+)/calmodulin (CaM)-dependent protein kinase after rises in intracellular Ca(2+), we measured enzymatic activity that phosphorylates SRF (designated SRF kinase activity). Homogenates from 7-day-hypertrophied anterior latissimus dorsi muscles of roosters had more Ca(2+)-independent SRF kinase activity than their respective control muscles. However, no differences were noted in Ca(2+)/CaM-dependent SRF kinase activity between control and trained muscles. To determine whether the Ca(2+)-independent and Ca(2+)/CaM-dependent forms of Ca(2+)/CaM-dependent protein kinase II (CaMKII) might contribute to some of the SRF kinase activity, autocamtide-3, a synthetic substrate that is specific for CaMKII, was employed. While the Ca(2+)-independent form of CaMKII was increased, like the Ca(2+)-independent form of SRF kinase, no alteration in CaMKII occurred at 7 days of stretch overload. These observations suggest that some of SRF phosphorylation by skeletal muscle extracts could be due to CaMKII. To determine whether this adaptation was specific to the exercise type (i.e., hypertrophy), similar measurements were made in the white vastus lateralis muscle of rats that had completed 2 wk of voluntary running. Although Ca(2+)-independent SRF kinase was increased, no alteration occurred in Ca(2+)/CaM-dependent SRF kinase activity. Thus any role of Ca(2+)-independent SRF kinase signaling has downstream modulators specific to the exercise phenotype.

NASA Program Fundamental Space Biology↗

NASA NTRS2004

Electron Spin Dephasing and Decoherence by Interaction with Nuclear Spins in Self-Assembled Quantum Dots

Electron spin dephasing and decoherence by its interaction with nuclear spins in self-assembled quantum dots are investigated in the framework of the empirical tight-binding model. Electron spin dephasing in an ensemble of dots is induced by the inhomogeneous precession frequencies of the electron among dots, while electron spin decoherence in a single dot arises from the inhomogeneous precession frequencies of nuclear spins in the dot. For In(x)Ga(1-x) As self-assembled dots containing ~30000 nuclei, the dephasing and decoherence times are predicted to be on the order of 100 ps and 1 (micro)s.

ensemble dephasing↗

NASA NTRS2002

Isolation and characterization of a novel calmodulin-binding protein from potato

Tuberization in potato is controlled by hormonal and environmental signals. Ca(2+), an important intracellular messenger, and calmodulin (CaM), one of the primary Ca(2+) sensors, have been implicated in controlling diverse cellular processes in plants including tuberization. The regulation of cellular processes by CaM involves its interaction with other proteins. To understand the role of Ca(2+)/CaM in tuberization, we have screened an expression library prepared from developing tubers with biotinylated CaM. This screening resulted in isolation of a cDNA encoding a novel CaM-binding protein (potato calmodulin-binding protein (PCBP)). Ca(2+)-dependent binding of the cDNA-encoded protein to CaM is confirmed by (35)S-labeled CaM. The full-length cDNA is 5 kb long and encodes a protein of 1309 amino acids. The deduced amino acid sequence showed significant similarity with a hypothetical protein from another plant, Arabidopsis. However, no homologs of PCBP are found in nonplant systems, suggesting that it is likely to be specific to plants. Using truncated versions of the protein and a synthetic peptide in CaM binding assays we mapped the CaM-binding region to a 20-amino acid stretch (residues 1216-1237). The bacterially expressed protein containing the CaM-binding domain interacted with three CaM isoforms (CaM2, CaM4, and CaM6). PCBP is encoded by a single gene and is expressed differentially in the tissues tested. The expression of CaM, PCBP, and another CaM-binding protein is similar in different tissues and organs. The predicted protein contained seven putative nuclear localization signals and several strong PEST motifs. Fusion of the N-terminal region of the protein containing six of the seven nuclear localization signals to the reporter gene beta-glucuronidase targeted the reporter gene to the nucleus, suggesting a nuclear role for PCBP.

NASA Discipline Plant Biology↗

DOE OSTI2022

Defining the HIV Capsid Binding Site of Nucleoporin 153

The human immunodeficiency virus (HIV) can infect nondividing cells by interacting with the host nuclear pore complex. The host nuclear pore protein NUP153 directly interacts with the HIV capsid to promote viral nuclear entry.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Perturbative Quantum Monte Carlo Method for Nuclear Physics

While first order perturbation theory is routinely used in quantum Monte Carlo (QMC) calculations, higher-order terms present significant numerical challenges. We present a new approach for computing perturbative corrections in projection QMC calculations. Here we demonstrate the method by computing nuclear ground state energies up to second order for a realistic chiral interaction. We calculate the binding energies of several light nuclei up to 16 O by expanding the Hamiltonian around the Wigner SU(4) limit and find good agreement with data. In contrast to the natural ordering of the perturbative series, we find remarkably large second-order energy corrections. This occurs because the perturbing interactions break the symmetries of the unperturbed Hamiltonian. Our method is free from the sign problem and can be applied to QMC calculations for many-body systems in nuclear physics, condensed matter physics, ultracold atoms, and quantum chemistry.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

NASA NTRS1984

Binding constants of phenylalanine for the four mononucleotides

Earlier work has shown that several properties of amino acids correlate directly with properties of their anticodonic nucleotides. Furthermore, in precipitation studies with thermal proteinoids and homopolyribonucleotides, an anticodonic preference was displayed between Lys-rich, Pro-rich and Gly-rich thermal proteinoids and their anticodonic polyribonucleotides. However, Phe-rich thermal proteinoid displayed a preference for its codonic nucleotide, poly U. This inconsistency seemed to be explained by a folding in of the hydrophobic residues of Phe causing the proteinoid to appear more hydrophilic. The present work used nuclear magnetic resonance techniques to resolve a limited question: to which of the four nucleotides does Phe bind most strongly? The results show quite clearly that Phe binds most strongly to its anticodonic nucleotide, AMP.

Khaled, M. A.↗

DOE OSTI2021

Rigorous constraints on three-nucleon forces in chiral effective field theory from fast and accurate calculations of few-body observables

We explore the constraints on the three-nucleon force (3NF) of chiral effective field theory (χ EFT) that are provided by bound-state observables in the A = 3 and A = 4 sectors. Our statistically rigorous analysis incorporates experimental error, computational method uncertainty, and the uncertainty due to truncation of the χ EFT expansion at next-to-next-to-leading order. A consistent solution for the 3 H binding energy, the 4 He binding energy and radius, and the 3 H β-decay rate can only be obtained if χ EFT truncation errors are included in the analysis. Here, the β-decay rate is the only one of these that yields a nondegenerate constraint on the 3NF low-energy constants, which makes it crucial for the parameter estimation. We use eigenvector continuation for fast and accurate emulation of no-core shell model calculations of the few-nucleon observables. This facilitates sampling of the posterior probability distribution, allowing us to also determine the distributions of the parameters that quantify the truncation error. We find a χ EFT expansion parameter of Q = 0.33 ± 0.06 for these observables.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

NASA NTRS1972

Deformed Brueckner-Hartree-Fock calculations

The renormalized Brueckner-Hartree-Fock (RBHF) theory for many-body nuclear systems is generalized to permit calculations for intrinsic states having permanent deformation. Both Hartree-Fock and Brueckner self-consistencies are satisfied, and details of the numerical techniques are discussed. The Hamada-Johnston interaction is used in a study of deformations, binding, size, and separation energies for several nuclei. Electromagnetic transition rates, moments, and electron scattering form factors are calculated using nuclear wave functions obtained by angular momentum projection. Comparison is made to experiment as well as to predictions of ordinary and density-dependent Hartree-Fock Theory.

Ford, W. F.↗

NASA NTRS1972

Deformed Brueckner-Hartree-Fock calculations.

The renormalized Brueckner-Hartree-Fock (RBHF) theory for many-body nuclear systems has been generalized to permit calculations for intrinsic states having permanent deformation. Both Hartree-Fock and Brueckner self-consistencies are satisfied, and details of the numerical techniques are discussed. The Hamada-Johnston interaction is used in a study of deformations, binding, size, and separation energies for several nuclei. Electromagnetic transition rates, moments, and electron scattering form factors are calculated using nuclear wave functions obtained by angular momentum projection. Comparison is made to experiment as well as to predictions of ordinary and density-dependent Hartree-Fock theory.

Ford, W. F.↗

DOE OSTI2021

HNRNPUL1 inhibits cisplatin sensitivity of esophageal squamous cell carcinoma through regulating the formation of circMAN1A2

Highlights: • HNRNPUL1 is an independent prognostic factor of ESCC patients receiving platinum-based chemotherapy. • Knockdown of HNRNPUL1 enhances cisplatin sensitivity of ESCC cells. • HNRNPUL1 inhibits the cisplatin sensitivity of ESCC cells by regulating the formation of circMAN1A2. Cisplatin (CDDP) is widely used for chemotherapy of esophageal squamous cell carcinoma (ESCC) but the drug resistance limits its therapeutic benefit. Heterogeneous nuclear ribonucleoprotein U-like 1 (HNRNPUL1) belongs to the family of RNA-binding proteins (RBPs) and is involved in DNA damage repair. To investigate whether and how HNRNPUL1 affects CDDP resistance of ESCC, we evaluated the expression of HNRNPUL1 and found that it was associated with recurrence in ESCC patients receiving postoperative platinum-based chemotherapy and was an independent prognostic factor for disease-free survival (DFS). Besides, we showed that the reduced expression of HNRNPUL1 enhanced the CDDP sensitivity of ESCC cells. Furthermore, RNA immunoprecipitation coupled with high-throughput sequencing (RIP-seq) were performed and a range of HNRNPUL1-binding RNAs influenced by CDDP treatment were identified followed by bioinformatics analysis. In terms of mechanism, we found that HNRNPUL1 inhibited CDDP sensitivity of ESCC cells by regulating the CDDP sensitivity-inhibited circular RNA (circRNA) MAN1A2 formation. Taken together, our results first demonstrated the role of HNRNPUL1 in CDDP resistance of ESCC and suggested that HNRNPUL1 may be a potential target of ESCC chemotherapy.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Improved naive Bayesian probability classifier in predictions of nuclear mass

Recently, novel statistical methods such as neural networks and Bayesian learning methods are implemented to describe the nuclear masses. Based on previous studies, an improved naive Bayesian probability (iNBP) classifier is proposed to study the nuclear masses by refining the results of sophisticated nuclear models. In the iNBP method, the prediction for nuclear masses is treated as a classification problem. The residuals are classified into several groups to generate prior and conditional probabilities, and the posterior probabilities are further determined by the Bayesian formula. We choose the expectation with maximum probability as the final prediction. Reliability of the iNBP method is assessed by analyzing the global optimizations and the extrapolating capabilities. Here, the iNBP method exhibits impressive improvements on global descriptions for different mass models. Moreover, the method shows robust extrapolating capabilities. Results demonstrate the iNBP method can be applied to predict the nuclear masses of unknown regions. Considering the local mass relations, the iNBP method can offer considerable fine-tuning of the mass descriptions from nuclear models. The methodology proposed in this paper can also be applied to other model-based extrapolations of nuclear observables.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗