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At least 919 records · Page 51

Status of Lattice QCD Calculations of One and Two-Nucleon Matrix Elements

Lattice QCD calculations of basic hadronic quantities are now often performed with systematic control over the physical pion mass, continuum and infinite volume limits. This progress signals a new era in which lattice QCD will be used to compute basic properties of hadrons, nucleons and light nuclei directly from the Standard Model (SM). In particular, we will be able to use lattice QCD, combined with Effective Field Theory, to make quantitative statements about the interaction of SM matter and potential beyond the SM physics ranging from direct dark matter detection to permanent electric dipole moments. I will briefly review the status and challenges of lattice QCD calculations of select one- and two-nucleon matrix elements. These calculations are significantly more challenging than the basic quantities computed with all systematics controlled, but substantial progress is being made.

Walker-Loud, Andre↗

Probing Lipophilic Adamantyl Group as the P1-Ligand for HIV-1 Protease Inhibitors: Design, Synthesis, Protein X-ray Structural Studies, and Biological Evaluation

A series of potent HIV-1 protease inhibitors with a lipophilic adamantyl P1 ligand have been designed, synthesized, and evaluated. We have developed an enantioselective synthesis of adamantane-derived hydroxyethylamine isosteres utilizing Sharpless asymmetric epoxidation as the key step. Various inhibitors incorporating P1-adamantylmethyl in combination with P2 ligands such as 3-(R)-THF, 3-(S)-THF, bis-THF, and THF-THP were examined. The S1' pocket was also probed with phenyl and phenylmethyl ligands. Inhibitor 15d, with an isobutyl P1' ligand and a bis-THF P2 ligand, proved to be the most potent of the series. Lastly, the cLogP value of inhibitor 15d is improved compared to inhibitor 2 with a phenylmethyl P1-ligand. X-ray structural studies of 15d, 15h, and 15i with HIV-1 protease complexes revealed molecular insight into the inhibitor–protein interaction.

59 BASIC BIOLOGICAL SCIENCES↗

Isolation of Two Agostic Isomers of an Organometallic Cation: Different Structures and Colors

Two isomers of [CpMo(CO)2(PiPr3)]+ were isolated, and both were characterized by x-ray crystallography and spectroscopic data. The two differ in the location of the agostic interaction with the metal, from either the CH (methine) or CH3 (methyl) group of the ligand. We thank the U.S. Department of Energy (DOE), Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences for support of this work. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle. The computational studies were performed using EMSL, a national scientific user facility sponsored by the DOE’s Office of Biological and Environmental Research and located at PNNL.

agostic interactions↗

Modeling Host-Pathogen Interactions in the Context of the Microenvironment: Three-Dimensional Cell Culture Comes of Age

Tissues and organs provide the structural and biochemical landscapes upon which microbial pathogens and commensals function to regulate health and disease. While flat two-dimensional (2-D) monolayers composed of a single cell type have provided important insight into understanding host-pathogen interactions and infectious disease mechanisms, these reductionist models lack many essential features present in the native host microenvironment that are known to regulate infection, including three-dimensional (3-D) architecture, multicellular complexity, commensal microbiota, gas exchange and nutrient gradients, and physiologically relevant biomechanical forces (e.g., fluid shear, stretch, compression). Here, a major challenge in tissue engineering for infectious disease research is recreating this dynamic 3-D microenvironment (biological, chemical, and physical/mechanical) to more accurately model the initiation and progression of host-pathogen interactions in the laboratory. Here we review selected 3-D models of human intestinal mucosa, which represent a major portal of entry for infectious pathogens and an important niche for commensal microbiota. We highlight seminal studies that have used these models to interrogate host-pathogen interactions and infectious disease mechanisms, and we present this literature in the appropriate historical context. Models discussed include 3-D organotypic cultures engineered in the rotating wall vessel (RWV) bioreactor, extracellular matrix (ECM)-embedded/organoid models, and organ-on-a-chip (OAC) models. Collectively, these technologies provide a more physiologically relevant and predictive framework for investigating infectious disease mechanisms and antimicrobial therapies at the intersection of the host, microbe, and their local microenvironments.

3-D↗

Distance‐based reconstruction of protein quaternary structures from inter‐chain contacts

Abstract Predicting the quaternary structure of protein complex is an important problem. Inter‐chain residue‐residue contact prediction can provide useful information to guide the ab initio reconstruction of quaternary structures. However, few methods have been developed to build quaternary structures from predicted inter‐chain contacts. Here, we develop the first method based on gradient descent optimization (GD) to build quaternary structures of protein dimers utilizing inter‐chain contacts as distance restraints. We evaluate GD on several datasets of homodimers and heterodimers using true/predicted contacts and monomer structures as input. GD consistently performs better than both simulated annealing and Markov Chain Monte Carlo simulation. Starting from an arbitrarily quaternary structure randomly initialized from the tertiary structures of protein chains and using true inter‐chain contacts as input, GD can reconstruct high‐quality structural models for homodimers and heterodimers with average TM‐score ranging from 0.92 to 0.99 and average interface root mean square distance from 0.72 Å to 1.64 Å. On a dataset of 115 homodimers, using predicted inter‐chain contacts as restraints, the average TM‐score of the structural models built by GD is 0.76. For 46% of the homodimers, high‐quality structural models with TM‐score ≥ 0.9 are reconstructed from predicted contacts. There is a strong correlation between the quality of the reconstructed models and the precision and recall of predicted contacts. Only a moderate precision or recall of inter‐chain contact prediction is needed to build good structural models for most homodimers. Moreover, GD improves the quality of quaternary structures predicted by AlphaFold2 on a Critical Assessment of Techniques for Protein Structure Prediction–Critical Assessments of Predictions of Interactions dataset.

59 BASIC BIOLOGICAL SCIENCES↗

Multiple CaMKII Binding Modes to the Actin Cytoskeleton Revealed by Single-Molecule Imaging

Localization of the Ca2þ/calmodulin-dependent protein kinase II (CaMKII) to dendritic spine synapses is determined in part by the actin cytoskeleton. We determined binding of GFP-tagged CaMKII to tag-RFP-labeled actin cytoskeleton within live cells using total internal reflection fluorescence microscopy and single-molecule tracking. Stepwise photobleaching showed that CaMKII formed oligomeric complexes. Photoactivation experiments demonstrated that diffusion out of the evanescent field determined the track lifetimes. Latrunculin treatment triggered a coupled loss of actin stress fibers and the colocalized, long-lived CaMKII tracks. The CaMKIIa (a) isoform, which was previously thought to lack F-actin interactions, also showed binding, but this was threefold weaker than that observed for CaMKIIb (b). The bE0 splice variant bound more weakly than a, showing that binding by b depends critically on the interdomain linker. The mutations bT287D and aT286D, which mimic autophosphorylation states, also abolished F-actin binding. Autophosphorylation triggers autonomous CaMKII activity, but does not impair GluN2B binding, another important synaptic protein interaction of CaMKII. The CaMKII inhibitor tatCN21 or CaMKII mutations that inhibit GluN2B association by blocking binding of ATP (bK43R and aK42M) or Ca2þ/calmodulin (bA303R) had no effect on the interaction with F-actin. These results provide the first rationale for the reduced synaptic spine localization of the aT286D mutant, indicating that transient F-actin binding contributes to the synaptic localization of the CaMKIIa isoform. The track lifetime distributions had a stretched exponential form consistent with a heterogeneously diffusing population. This heterogeneity suggests that CaMKII adopts different F-actin binding modes, which is most easily rationalized by multiple subunit contacts between the CaMKII dodecamer and the F-actin cytoskeleton that stabilize the initial weak (micromolar) monovalent interaction.

59 BASIC BIOLOGICAL SCIENCES↗

From single cell to spatial multi-omics: unveiling molecular mechanisms in dynamic and heterogeneous systems

Single-cell multi-omics and spatial technology have been widely applied to biomedical studies and recently to environmental studies. Here, the cell size detected by single-cell omics ranges from ~2 µm (e.g., Bacillus subtilis) to ~120 µm (e.g., human oocytes). Simultaneous detection of single-cell multi-omics is available to human and plant tissues while limited to microbial samples. Spatial technology enables mapping the detected biomolecules in situ. The recent advances in MALDI-MSI and micro/nanoPOTS for the first time allow the application of spatial multi-omics in highly heterogeneous environmental samples composed of plants, fungi, and bacteria. We envision that these technologies will continue to advance our understanding of unique cell types, their developmental trajectory, and the intercellular signaling and interaction within biological samples.

59 BASIC BIOLOGICAL SCIENCES↗

Atomic-scale mechanisms of helium bubble hardening in iron

Generation of helium due to (n,α) transmutation reactions changes the response of structural materials to neutron irradiation. The whole process of radiation damage evolution is affected by He accumulation and leads to significant changes in the material s properties. A population of nanometric He-filled bubbles affects mechanical properties and the impact can be quite significant because of their high density. Understanding how these basic mechanisms affect mechanical properties is necessary for predicting radiation effects. In this paper we present an extensive study of the interactions between a moving edge dislocation and bubbles using atomic-scale modeling. We focus on the effect of He bubble size and He concentration inside bubbles. Thus, we found that ability of bubbles to act as an obstacle to dislocation motion is close to that of voids when the He-to-vacancy ratio is in the range from 0 to 1. A few simulations made at higher He contents demonstrated that the interaction mechanism is changed for over-pressurized bubbles and they become weaker obstacles. The results are discussed in light of post-irradiation materials testing.

36 MATERIALS SCIENCE↗

Iron(III)–Oxo Cluster Chemistry with Dimethylarsinate Ligands: Structures, Magnetic Properties, and Computational Studies

A program has been initiated to develop Fe III /oxo cluster chemistry with the ‘pseudo-carboxylate’ ligand dimethylarsinate (Me 2 AsO 2 - ) for comparison with the well investigated Fe III /oxo/carboxylate cluster area. The synthesis and characterization of three polynuclear Fe III complexes are reported, [Fe 12 O 4 (O 2 C t Bu) 8 (O 2 AsMe 2 ) 17 (H 2 O) 3 ]Cl 3 (1), Na 2 [Fe 12 Na 2 O 4 (O 2 AsMe 2 ) 20 (NO 3 ) 6 (Me 2 AsO 2 H) 2 (H 2 O) 4 ](NO 3 ) 6 (2) and [Fe 3 (O 2 AsMe 2 ) 6 (Me 2 AsO 2 H) 2 (hqn) 2 ](NO 3 ) (3), where hqn is 8-hydroxyquinoline. The Fe 12 core of 1 is a type never previously encountered in Fe III carboxylate chemistry, consisting of two Fe 6 units each of which comprises two {Fe 3 (μ 3 -O 2- )} units bridged by three Me 2 AsO 2 - groups and linked into an Fe 12 loop structure by two anti-anti η 1 :η 1 :μ Me 2 AsO 2 - groups, a bridging mode extremely rare with carboxylates. 2 also consists of two Fe 6 units, differing in their ligation from those in 1, and this time linked together into a linear structure by a central {Na 2 (NO 3 ) 2 } bridging unit. 3 is a linear Fe 3 complex with no monoatomic bridges between Fe III ions, a very rare situation in Fe III chemistry with any ligands, and unprecedented in Fe carboxylate chemistry. The distinct differences observed in arsinate vs carboxylate ligation modes are rationalized largely based on the greater basicity of the former vs the latter. Variable-temperature dc and ac magnetic susceptibility data reveal all Fe 2 pairwise interactions to be antiferromagnetic. For 1 and 2, the different J ij couplings were estimated by use of a magnetostructural correlation for high nuclearity Fe III -oxo clusters and by density functional theory calculations using broken symmetry methods, allowing identification of their relative spin vector alignments and thus rationalization of their S = 0 ground states. The J ij values were then used as input values to give excellent fits of the experimental χM T vs T data. For 3, the fits of the experimental χM T vs T data to the Van Vleck equation or with PHI gave a very weak J 12 = -0.8(1) cm -1 (H = –2JŠ i ·Š j convention) between adjacent Fe III ions, and an S = 5/2 ground state. Furthermore, these initial Fe III arsinate complexes also provide structural parameters that help validate literature assignments of arsinate binding modes to iron oxide/hydroxide minerals as part of environmental concerns of using arsenic-containing herbicides in agriculture.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Methionine 170 is an Environmentally Sensitive Membrane Anchor in the Disordered HVR of K-Ras4B

Ras protein colocalization at the plasma membrane is implicated in the activation of signaling cascades that promote cell growth, survival, and motility. However, the mechanisms that underpin Ras self-association remain unclear. We use molecular dynamics simulations to show how basic and hydrophobic components of the disordered C-terminal membrane tether of K-Ras4B combine to regulate its membrane interactions. Specifically, anionic lipids attract lysine residues to the membrane surface, thereby splitting the peptide population into two states that exchange on the microsecond time scale. These states differ in the membrane insertion of a methionine residue, which is influenced by local membrane composition. As a result, these states may impose context-dependent biases on the disposition of Ras’ signaling domain, with possible implications for the accessibility of its effector binding surfaces. Furthermore, we investigate Ras’ ability to nanocluster by fly-casting for patches of anionic lipids and find that while anionic lipids promote the intermolecular association of K-Ras4B membrane tethers, at short range this appears to be a passive process in which anionic lipids electrostatically screen these cationic peptides to mitigate their natural repulsion. Together with the sub-microsecond stability of interpeptide contacts, this result suggests that experimentally observed K-Ras4B nanoclustering is not driven by direct intermolecular contact of its membrane tethers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Differential Coexpression Analysis Reveals Extensive Rewiring of Arabidopsis Gene Coexpression in Response to Pseudomonas syringae Infection

Plant defense responses to pathogens involve massive transcriptional reprogramming. Recently, differential coexpression analysis has been developed to study the rewiring of gene networks through microarray data, which is becoming an important complement to traditional differential expression analysis. Using time-series microarray data of Arabidopsis thaliana infected with Pseudomonas syringae, we analyzed Arabidopsis defense responses to P. syringae through differential coexpression analysis. Overall, we found that differential coexpression was a common phenomenon of plant immunity. Genes that were frequently involved in differential coexpression tend to be related to plant immune responses. Importantly, many of those genes have similar average expression levels between normal plant growth and pathogen infection but have different coexpression partners. By integrating the Arabidopsis regulatory network into our analysis, we identified several transcription factors that may be regulators of differential coexpression during plant immune responses. We also observed extensive differential coexpression between genes within the same metabolic pathways. Several metabolic pathways, such as photosynthesis light reactions, exhibited significant changes in expression correlation between normal growth and pathogen infection. Taken together, differential coexpression analysis provides a new strategy for analyzing transcriptional data related to plant defense responses and new insights into the understanding of plant-pathogen interactions.

59 BASIC BIOLOGICAL SCIENCES↗

RCNP E398 {sup 16}O,{sup 12}C(p,p’) experiment: Measurement of the γ-ray emission probability from giant resonances in relation to {sup 16}O,{sup 12}C(ν,ν’) reactions

We propose to measure the γ-ray emission probability from excited states above 5 MeV including giant resonance of {sup 16}O and {sup 12}C as a function of excitation energy in 1-MeV step. Here, we measure both the excitation energy (E{sub x}=5-30MeV) at the forward scattering angles (0°-3°) of the {sup 16}O, {sup 12}C (p, p’) reaction using Grand-Raiden Spectrometer and the energy of γ-rays (E{sub γ}) using an array of NaI(Tl) counters. The purpose of the experiment is to provide the basic and important information not only for the γ-ray production from primary neutral-current neutrino-oxygen (-carbon) interactions but also for that from the secondary hadronic (neutron-oxygen and -carbon) interactions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Mechanism of the G-protein mimetic nanobody binding to a muscarinic G-protein-coupled receptor

Protein–protein binding is key in cellular signaling processes. Molecular dynamics (MD) simulations of protein–protein binding, however, are challenging due to limited timescales. In particular, binding of the medically important G-protein-coupled receptors (GPCRs) with intracellular signaling proteins has not been simulated with MD to date. Here, we report a successful simulation of the binding of a G-protein mimetic nanobody to the M 2 muscarinic GPCR using the robust Gaussian accelerated MD (GaMD) method. Through long-timescale GaMD simulations over 4,500 ns, the nanobody was observed to bind the receptor intracellular G-protein-coupling site, with a minimum rmsd of 2.48 Å in the nanobody core domain compared with the X-ray structure. Binding of the nanobody allosterically closed the orthosteric ligand-binding pocket, being consistent with the recent experimental finding. In the absence of nanobody binding, the receptor orthosteric pocket sampled open and fully open conformations. The GaMD simulations revealed two low-energy intermediate states during nanobody binding to the M 2 receptor. The flexible receptor intracellular loops contribute remarkable electrostatic, polar, and hydrophobic residue interactions in recognition and binding of the nanobody. As a result, these simulations provided important insights into the mechanism of GPCR–nanobody binding and demonstrated the applicability of GaMD in modeling dynamic protein–protein interactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The Structure of Sucrose Synthase-1 from Arabidopsis thaliana and Its Functional Implications

Sucrose transport is the central system for the allocation of carbon resources in vascular plants. During growth and development, plants control carbon distribution by coordinating sites of sucrose synthesis and cleavage in different plant organs and different cellular locations. Sucrose synthase, which reversibly catalyzes sucrose synthesis and cleavage, provides a direct and reversible means to regulate sucrose flux. Depending on the metabolic environment, sucrose synthase alters its cellular location to participate in cellulose, callose, and starch biosynthesis through its interactions with membranes, organelles, and cytoskeletal actin. The x-ray crystal structure of sucrose synthase isoform 1 from Arabidopsis thaliana (AtSus1) has been determined as a complex with UDP-glucose and as a complex with UDP and fructose, at 2.8- and 2.85-{angstrom} resolutions, respectively. The AtSus1 structure provides insights into sucrose catalysis and cleavage, as well as the regulation of sucrose synthase and its interactions with cellular targets.

59 BASIC BIOLOGICAL SCIENCES↗

Toxin-Antitoxin Systems Reflect Community Interactions Through Horizontal Gene Transfer

Bacterial evolution through horizontal gene transfer (HGT) reflects their community interactions. In this way, HGT networks do well at mapping community interactions, but offer little toward controlling them—an important step in the translation of synthetic strains into natural contexts. Toxin–antitoxin (TA) systems serve as ubiquitous and diverse agents of selection; however, their utility is limited by their erratic distribution in hosts. Here we examine the heterogeneous distribution of TAs as a consequence of their mobility. By systematically mapping TA systems across a 10,000 plasmid network, we find HGT communities have unique and predictable TA signatures. We propose these TA signatures arise from plasmid competition and have further potential to signal the degree to which plasmids, hosts, and phage interact. To emphasize these relationships, we construct an HGT network based solely on TA similarity, framing specific selection markers in the broader context of bacterial communities. This work both clarifies the evolution of TA systems and unlocks a common framework for manipulating community interactions through TA compatibility.

59 BASIC BIOLOGICAL SCIENCES↗

Building an extensible cell wall

Abstract This article recounts, from my perspective of four decades in this field, evolving paradigms of primary cell wall structure and the mechanism of surface enlargement of growing cell walls. Updates of the structures, physical interactions, and roles of cellulose, xyloglucan, and pectins are presented. This leads to an example of how a conceptual depiction of wall structure can be translated into an explicit quantitative model based on molecular dynamics methods. Comparison of the model’s mechanical behavior with experimental results provides insights into the molecular basis of complex mechanical behaviors of primary cell wall and uncovers the dominant role of cellulose–cellulose interactions in forming a strong yet extensible network.

59 BASIC BIOLOGICAL SCIENCES↗

First High-Throughput Evaluation of Dark Matter Detector Materials

In this work we perform the first high-throughput search and evaluation of materials that can serve as excellent low-mass dark matter detectors. Using properties of close to 1000 materials from the Materials Project database, we project the sensitivity in dark matter parameter space for experiments constructed from each material, including both absorption and scattering processes between dark matter and electrons. Using the anisotropic materials in the dataset, we further compute the level of daily modulation in interaction rates and the resulting directional sensitivities, highlighting materials with prospects to detect the dark matter wind. Our methods provide the basic tools for the data-driven design of dark matter detectors, and our findings lay the groundwork for the next generation of highly optimized direct searches for dark matter as light as the keV scale. This represents a major step in the application of results from condensed matter physics to dark matter search design.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Windowed multipole representation of R -matrix cross sections

Nuclear cross sections are basic inputs to any nuclear computation. Campaigns of experiments are fitted with the parametric R-matrix model of quantum nuclear interactions, and the resulting cross sections are documented—both pointwise and as resonance parameters (with uncertainties)—in standard evaluated nuclear data libraries (ENDF, JEFF, BROND, JENDL, CENDL, TENDL): these constitute our common knowledge of fundamental low-energy nuclear cross sections. In the past decade, a collaborative effort has been deployed to establish a new nuclear cross-section library format—the Windowed Multipole Library—with the goal of considerably reducing the computational cost of cross-section calculations in nuclear transport simulations. This work lays the theoretical foundations underpinning these efforts. From general R-matrix scattering theory, we derive the windowed multipole representation of nuclear cross sections. Though physically and mathematically equivalent to R-matrix cross sections, the windowed multipole representation is particularly well suited for subsequent temperature treatment of angle-integrated cross sections, in particular Doppler broadening, which is the averaging of cross sections over the thermal motion of the target atoms. Doppler broadening is of critical importance in neutron transport applications, as it ensures the stability of many nuclear reactors (negative thermal reactivity). Yet, Doppler broadening of nuclear cross sections has been a considerable bottleneck for nuclear transport computations, often requiring memory-costly pretabulations. We show that the windowed multipole representation can perform accurate Doppler broadening analytically (up to the first reaction threshold), from which we derive cross-section temperature derivatives to any order—all computable on the fly (without precalculations stored in memory). Furthermore, we here establish a way of converting the R-matrix resonance parameters uncertainty (covariance matrices) into windowed multipole parameters uncertainty. We show that generating stochastic nuclear cross sections by sampling from the resulting windowed multipole covariance matrix can reproduce the cross-section uncertainty in the original nuclear data file. The windowed multipole representation is therefore a novel nuclear physics formalism able to generate Doppler broadened stochastic nuclear cross sections on the fly, unlocking breakthrough computational gains for nuclear computations. Through this foundational paper, we hope to make the windowed multipole representation accessible, reproducible, and usable for the nuclear physics community, as well as provide the theoretical basis for future research on expanding its capabilities.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗