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Role of hypoxia-inducible factor-1 in transcriptional activation of ceruloplasmin by iron deficiency
A role of the copper protein ceruloplasmin (Cp) in iron metabolism is suggested by its ferroxidase activity and by the tissue iron overload in hereditary Cp deficiency patients. In addition, plasma Cp increases markedly in several conditions of anemia, e.g. iron deficiency, hemorrhage, renal failure, sickle cell disease, pregnancy, and inflammation. However, little is known about the cellular and molecular mechanism(s) involved. We have reported that iron chelators increase Cp mRNA expression and protein synthesis in human hepatocarcinoma HepG2 cells. Furthermore, we have shown that the increase in Cp mRNA is due to increased rate of transcription. We here report the results of new studies designed to elucidate the molecular mechanism underlying transcriptional activation of Cp by iron deficiency. The 5'-flanking region of the Cp gene was cloned from a human genomic library. A 4774-base pair segment of the Cp promoter/enhancer driving a luciferase reporter was transfected into HepG2 or Hep3B cells. Iron deficiency or hypoxia increased luciferase activity by 5-10-fold compared with untreated cells. Examination of the sequence showed three pairs of consensus hypoxia-responsive elements (HREs). Deletion and mutation analysis showed that a single HRE was necessary and sufficient for gene activation. The involvement of hypoxia-inducible factor-1 (HIF-1) was shown by gel-shift and supershift experiments that showed HIF-1alpha and HIF-1beta binding to a radiolabeled oligonucleotide containing the Cp promoter HRE. Furthermore, iron deficiency (and hypoxia) did not activate Cp gene expression in Hepa c4 hepatoma cells deficient in HIF-1beta, as shown functionally by the inactivity of a transfected Cp promoter-luciferase construct and by the failure of HIF-1 to bind the Cp HRE in nuclear extracts from these cells. These results are consistent with in vivo findings that iron deficiency increases plasma Cp and provides a molecular mechanism that may help to understand these observations.
Diabatic Hamiltonian matrix elements made simple
With a view to applying the generator coordinate method to large configuration spaces, we propose a simple approximate formula to compute diabatic many-body matrix elements without having to evaluate two-body interaction matrix elements. Here, the method is illustrated with two analytically solvable Hamiltonians based on the harmonic oscillator.
Constraining nuclear mass models using 𝑟-process observables with multiobjective optimization
Modeling nuclear masses, particularly for nuclei far from stability, remains a key objective in nuclear physics. One contemporary approach is machine learning (ML), which trains on experimental data, but can suffer large errors when extrapolating toward neutron-rich species. In nature, such masses shape observables for the rapid neutron capture process (𝑟 process), which in principle could inform ML models. Here, we introduce a multiobjective optimization approach using the Pareto front algorithm. We show that this technique, capable of identifying models that generate 𝑟-process abundances aligning with both solar and stellar data, is a promising method to select ML models with reliable extrapolation power.
High-precision mass measurement of Si 24 and a refined determination of the r p process at the A = 22 waiting point
We report a high-precision mass measurement of 24 Si, performed with the Low Energy Beam and Ion Trap (LEBIT) facility at the National Superconducting Cyclotron Laboratory. The atomic mass excess, 10 753.8 (37) keV, is a factor of 5 more precise than previous results. This substantially reduces the uncertainty of the 23 Al(p ,γ) 24 Si reaction rate, which is a key part of the rapid proton capture (rp) process powering type I x-ray bursts. Furthermore, the updated rate constrains the onset temperature of the (α,p) process at the 22 Mg waiting point to a precision of 9%.
Zuotin, a putative Z-DNA binding protein in Saccharomyces cerevisiae
A putative Z-DNA binding protein, named zuotin, was purified from a yeast nuclear extract by means of a Z-DNA binding assay using [32P]poly(dG-m5dC) and [32P]oligo(dG-Br5dC)22 in the presence of B-DNA competitor. Poly(dG-Br5dC) in the Z-form competed well for the binding of a zuotin containing fraction, but salmon sperm DNA, poly(dG-dC) and poly(dA-dT) were not effective. Negatively supercoiled plasmid pUC19 did not compete, whereas an otherwise identical plasmid pUC19(CG), which contained a (dG-dC)7 segment in the Z-form was an excellent competitor. A Southwestern blot using [32P]poly(dG-m5dC) as a probe in the presence of MgCl2 identified a protein having a molecular weight of 51 kDa. The 51 kDa zuotin was partially sequenced at the N-terminal and the gene, ZUO1, was cloned, sequenced and expressed in Escherichia coli; the expressed zuotin showed similar Z-DNA binding activity, but with lower affinity than zuotin that had been partially purified from yeast. Zuotin was deduced to have a number of potential phosphorylation sites including two CDC28 (homologous to the human and Schizosaccharomyces pombe cdc2) phosphorylation sites. The hexapeptide motif KYHPDK was found in zuotin as well as in several yeast proteins, DnaJ of E.coli, csp29 and csp32 proteins of Drosophila and the small t and large T antigens of the polyoma virus. A 60 amino acid segment of zuotin has similarity to several histone H1 sequences. Disruption of ZUO1 in yeast resulted in a slow growth phenotype.
Cysteine Rich Intestinal Protein 2 is a copper-responsive regulator of skeletal muscle differentiation and metal homeostasis
Copper (Cu) is essential for respiration, neurotransmitter synthesis, oxidative stress response, and transcription regulation, with imbalances leading to neurological, cognitive, and muscular disorders. Here we show the role of a novel Cu-binding protein (Cu-BP) in mammalian transcriptional regulation, specifically on skeletal muscle differentiation using murine primary myoblasts. Utilizing synchrotron X-ray fluorescence-mass spectrometry, we identified murine cysteine-rich intestinal protein 2 (mCrip2) as a key Cu-BP abundant in both nuclear and cytosolic fractions. mCrip2 binds two to four Cu + ions with high affinity and presents limited redox potential. CRISPR/Cas9-mediated deletion of mCrip2 impaired myogenesis, likely due to Cu accumulation in cells. CUT&RUN and transcriptome analyses revealed its association with gene promoters, including MyoD1 and metallothioneins, suggesting a novel Cu-responsive regulatory role for mCrip2. Our work describes the significance of mCrip2 in skeletal muscle differentiation and metal homeostasis, expanding understanding of the Cu-network in myoblasts. Copper (Cu) is essential for various cellular processes, including respiration and stress response, but imbalances can cause serious health issues. This study reveals a new Cu-binding protein (Cu-BP) involved in muscle development in primary myoblasts. Using unbiased metalloproteomic techniques and high throughput sequencing, we identified mCrip2 as a key Cu-BP found in cell nuclei and cytoplasm. mCrip2 binds up to four Cu + ions and has a limited redox potential. Deleting mCrip2 using CRISPR/Cas9 disrupted muscle formation due to Cu accumulation. Further analyses showed that mCrip2 regulates the expression of genes like MyoD1, essential for muscle differentiation, and metallothioneins in response to copper supplementation. This research highlights the importance of mCrip2 in muscle development and metal homeostasis, providing new insights into the Cu-network in cells.
Role of karyopherin nuclear transport receptors in nuclear transport by nuclear trafficking peptide
Nuclear trafficking peptide (NTP), a cell-penetrating peptide (CPP) composed of 10 amino acids (aa) (RIFIHFRIGC), has potent nuclear trafficking activity. Recently, we established a protein-based cell engineering system by using NTP, but it remained elusive how NTP functions as a CPP with nuclear orientation. In the present study, we identified importin subunit β1 (IMB1) and transportin 1 (TNPO1) as cellular proteins underlying the activity of NTP. These karyopherin nuclear transport receptors were identified as candidate molecules by liquid chromatography/mass spectrometry analysis, and downregulation of each protein by small interfering RNA significantly reduced NTP activity (P < 0.01). Biochemical analyses revealed that NTP bound directly to both molecules, and the forced expression of an IMB1 fragment (296–516 aa) or TNPO1 fragment (1–297 aa), which both contain binding sites to NTP, reduced nuclear NTP-green fluorescent protein (GFP) levels when it was added to cell culture medium. NTP is derived from viral protein R (Vpr) of human immunodeficiency virus-1, and Vpr enters the nucleus and exerts pleiotropic functions. Notably, Vpr bound directly to IMB1 and TNPO1, and its function was significantly impaired by the forced expression of the 296–516-aa fragment of IMB1 and 1–297-aa fragment of TNPO1. Interestingly, NTP completely blocked the physical association of Vpr with IMB1 and TNPO1. Although the nuclear localization mechanism of Vpr remains unknown, our data suggest that NTP functions as a novel nuclear localization signal of Vpr.
Evolution of the nuclear spin-orbit splitting explored via the 32 Si( d,p ) 33 Si reaction using SOLARIS
The spin-orbit splitting between neutron 1p orbitals at 33 Si has been deduced using the single-neutron-adding (d,p) reaction in inverse kinematics with a beam of 32 Si, a long-lived radioisotope. Reaction products were analyzed by the newly implemented SOLARIS spectrometer at the reaccelerated-beam facility at the National Superconducting Cyclotron Laboratory. The measurements show reasonable agreement with shell-model calculations that incorporate modern cross-shell interactions, but they contradict the prediction of proton density depletion based on relativistic mean-field theory. The evolution of the neutron 1p-shell orbitals is systematically studied using the present and existing data in the isotonic chains of N = 17, 19, and 21. In each case, a smooth decrease in the separation of the 1p 3/2 - 1p 1/2 orbitals is seen as the respective p-orbitals approach zero binding, suggesting that the finite nuclear potential strongly influences the evolution of nuclear structure in this region.
Atrogin-1, a muscle-specific F-box protein highly expressed during muscle atrophy
Muscle wasting is a debilitating consequence of fasting, inactivity, cancer, and other systemic diseases that results primarily from accelerated protein degradation by the ubiquitin-proteasome pathway. To identify key factors in this process, we have used cDNA microarrays to compare normal and atrophying muscles and found a unique gene fragment that is induced more than ninefold in muscles of fasted mice. We cloned this gene, which is expressed specifically in striated muscles. Because this mRNA also markedly increases in muscles atrophying because of diabetes, cancer, and renal failure, we named it atrogin-1. It contains a functional F-box domain that binds to Skp1 and thereby to Roc1 and Cul1, the other components of SCF-type Ub-protein ligases (E3s), as well as a nuclear localization sequence and PDZ-binding domain. On fasting, atrogin-1 mRNA levels increase specifically in skeletal muscle and before atrophy occurs. Atrogin-1 is one of the few examples of an F-box protein or Ub-protein ligase (E3) expressed in a tissue-specific manner and appears to be a critical component in the enhanced proteolysis leading to muscle atrophy in diverse diseases.
Molecular binding in the cell surface Progress report, period ending 31 Dec. 1965
Microwave apparatus and nuclear magnetic resonance and electron paramagnetic resonance spectroscopy for elucidation of molecular binding in cell surface
MISPR : an open-source package for high-throughput multiscale molecular simulations
Computational tools provide a unique opportunity to study and design optimal materials by enhancing our ability to comprehend the connections between their atomistic structure and functional properties. However, designing materials with tailored functionalities is complicated due to the necessity to integrate various computational-chemistry software (not necessarily compatible with one another), the heterogeneous nature of the generated data, and the need to explore vast chemical and parameter spaces. The latter is especially important to avoid bias in scattered data points-based models and derive statistical trends only accessible by systematic datasets. Here, we introduce a robust high-throughput multi-scale computational infrastructure coined MISPR (Materials Informatics for Structure–Property Relationships) that seamlessly integrates classical molecular dynamics (MD) simulations with density functional theory (DFT). By enabling high-performance data analytics and coupling between different methods and scales, MISPR addresses critical challenges arising from the needs of automated workflow management and data provenance recording. The major features of MISPR include automated DFT and MD simulations, error handling, derivation of molecular and ensemble properties, and creation of output databases that organize results from individual calculations to enable reproducibility and transparency. In this work, we describe fully automated DFT workflows implemented in MISPR to compute various properties such as nuclear magnetic resonance chemical shift, binding energy, bond dissociation energy, and redox potential with support for multiple methods such as electron transfer and proton-coupled electron transfer reactions. The infrastructure also enables the characterization of large-scale ensemble properties by providing MD workflows that calculate a wide range of structural and dynamical properties in liquid solutions. MISPR employs the methodologies of materials informatics to facilitate understanding and prediction of phenomenological structure–property relationships, which are crucial to designing novel optimal materials for numerous scientific applications and engineering technologies.
Comparative analysis of KRAS4a and KRAS4b splice variants reveals distinctive structural and functional properties
KRAS, the most frequently mutated oncogene in human cancer, produces two isoforms, KRAS4a and KRAS4b, through alternative splicing. These isoforms differ in exon 4, which encodes the final 15 residues of the G-domain and hypervariable regions (HVRs), vital for trafficking and membrane localization. While KRAS4b has been extensively studied, KRAS4a has been largely overlooked. Our multidisciplinary study compared the structural and functional characteristics of KRAS4a and KRAS4b, revealing distinct structural properties and thermal stability. Position 151 influences KRAS4a’s thermal stability, while position 153 affects binding to RAF1 CRD protein. Nuclear magnetic resonance analysis identified localized structural differences near sequence variations and provided a solution-state conformational ensemble. Notably,KRAS4aexhibits substantial transcript abundance in bile ducts, liver, and stomach, with transcript levels approachingKRAS4bin the colon and rectum. Functional disparities were observed in full-length KRAS variants, highlighting the impact of HVR variations on interaction with trafficking proteins and downstream effectors like RAF and PI3K within cells.
Muon Catalyzed Fusion
Muon catalyzed fusion is a process in which a negatively charged muon combines with two nuclei of isotopes of hydrogen, e.g, a proton and a deuteron or a deuteron and a triton, to form a muonic molecular ion in which the binding is so tight that nuclear fusion occurs. The muon is normally released after fusion has taken place and so can catalyze further fusions. As the muon has a mean lifetime of 2.2 microseconds, this is the maximum period over which a muon can participate in this process. This article gives an outline of the history of muon catalyzed fusion from 1947, when it was first realised that such a process might occur, to the present day. It includes a description of the contribution that Drachrnan has made to the theory of muon catalyzed fusion and the influence this has had on the author's research.
Chelating platform for delivery of radionuclides
Siderocalin-metal chelator combinations that bind metallic radioisotopes used in nuclear medicine with high affinity are described. The high affinity siderocalin-metal chelator combinations include a number of chelator backbone arrangements with functional groups that coordinate with metals. The siderocalin-metal chelator combinations can be used to deliver radionuclides for imaging and therapeutic purposes.
Spectroscopic study of a possible $Λnn$ resonance and a pair of $ΣNN$ states using the $(e,e'K^+)$ reaction with a tritium target
Here, a mass spectroscopy experiment with a pair of nearly identical high resolution spectrometers and a tritium target was performed in Hall A at Jefferson Lab. Utilizing the (e,e'K + ) reaction, enhancements, which may correspond to a possible $\Lambda$nn resonance and a pair of ΣNN states, were observed with an energy resolution of about 1.21 MeV (σ), although greater statistics are needed to make definitive identifications. An experimentally measured Λnn state may provide a unique constraint in determining the Λn interaction, for which no scattering data exist. In addition, although bound A = 3 and 4 Σ hypernuclei have been predicted, only an A = 4 Σ hypernucleus ($^4_Σ$He) was found, utilizing the (K - ,π - ) reaction on a 4 He target. The possible bound ΣNN state is likely a Σ 0 nn state, although this has to be confirmed by future experiments.
Nuclear spectroscopy with heavy ion nucleon knockout and (p,2p) reactions
Knockout reactions with heavy ion targets in inverse kinematics, as well as “quasifree” (p,2p) and (p,pn) reactions are useful tools for nuclear spectroscopy. We report calculations on ab initio many-body wave functions based on the no-core shell model to study the nucleon removal reactions in light nuclei, including beryllium, carbon, and oxygen isotopic chains, and explore the importance of using an ab initio method. Our study helps to clarify how the extraction of spectroscopic factors from the experiments depend on the details of the many-body wave functions being probed. We show that recent advances with the ab initio method can provide more insights on the spectroscopy information extracted from experiments.
Ligand flexibility and binding pocket malleability cooperate to allow selective PXR activation by analogs of a promiscuous nuclear receptor ligand
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