Structural insights of non-canonical U.U pair and Hoogsteen interaction probed with Se atom
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59 BASIC BIOLOGICAL SCIENCES↗
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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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Retractile lysyl-tRNA synthetase-AIMP2 assembly in the human multi-aminoacyl-tRNA synthetase complex
Multi-aminoacyl-tRNA synthetase complex (MSC) is the second largest machinery for protein synthesis in human cells and also regulates multiple nontranslational functions through its components. Prior studies have shown that the MSC can respond to external signals by releasing its components to function outside it. The internal assembly is fundamental to MSC regulation. Here, using crystal structural analyses (at 1.88 Å resolution) along with molecular modeling, gel-filtration chromatography, and co-immunoprecipitation, we report that human lysyl-tRNA synthetase (LysRS) forms a tighter assembly with the scaffold protein aminoacyl-tRNA synthetase complex-interacting multifunctional protein 2 (AIMP2) than previously observed. Wefound that two AIMP2 N-terminal peptides form an antiparallel scaffold and hold two LysRS dimers through four binding motifs and additional interactions. Of note, the four catalytic subunits of LysRS in the tightly assembled complex were all accessible for tRNA recognition. We further noted that two recently reported human disease-associated mutations conflict with this tighter assembly, cause LysRS release from the MSC, and inactivate the enzyme. These findings reveal a previously unknown dimension of MSC subcomplex assembly and suggest that the retractility of this complex may be critical for its physiological functions.
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From Protein Design to the Energy Landscape of a Cold Unfolding Protein
Understanding protein folding is crucial for protein sciences. The conformational spaces and energy landscapes of cold (unfolded) protein states, as well as the associated transitions, are hardly explored. Furthermore, it is not known how structure relates to the cooperativity of cold transitions, if cold and heat unfolded states are thermodynamically similar, and if cold states play important roles for protein function. We created the cold unfolding 4-helix bundle DCUB1 with a de novo designed bipartite hydrophilic/hydrophobic core featuring a hydrogen bond network which extends across the bundle in order to study the relative importance of hydrophobic versus hydrophilic protein–water interactions for cold unfolding. Structural and thermodynamic characterization resulted in the discovery of a complex energy landscape for cold transitions, while the heat unfolded state is a random coil. Below ~0 °C, the core of DCUB1 disintegrates in a largely cooperative manner, while a near-native helical content is retained. The resulting cold core-unfolded state is compact and features extensive internal dynamics. Below -5 °C, two additional cold transitions are seen, that is, (i) the formation of a water-mediated, compact, and highly dynamic dimer, and (ii) the onset of cold helix unfolding decoupled from cold core unfolding. Our results suggest that cold unfolding is initiated by the intrusion of water into the hydrophilic core network and that cooperativity can be tuned by varying the number of core hydrogen bond networks. Protein design has proven to be invaluable to explore the energy landscapes of cold states and to robustly test related theories.
59 BASIC BIOLOGICAL SCIENCES↗
Synthesis, crystal structure, and magnetic properties of bis(aqua)[μ-(terepthalato-κo,κo´)]copper(II)monohydrate [Cu(C₈O₄)(OH₂)₂]·H₂O
A novel one dimensional Cu(II) coordination polymer [Cu(C₈O₄)(OH₂)₂] ·H₂O 1 has been synthesized and characterized by elemental analysis, IR spectroscopy, X-ray crystal diffraction and magnetic measurements. Single-crystal structural analysis shows that complex 1 consist of 1D Cu(II) chain containing threefold bridging ligands, one (syn–syn) carboxylate and two water molecules. The magnetic study of 1 has been investigated, indicating an overall antiferromagnetic interaction in the complex. - Graphical abstract: The complex [Cu(C₈O₄)(OH₂)₂] ·H₂O was prepared by the reaction of solid copper(II)basic carbonate with an aqueous solution of sodium terephthalate under heating at 50–60 {sup o}C after which it was allowed to crystallize at room temperature. The structure of the complex is distorted octahedral. Magnetic study of the complex reveals antiferromagnetic behaviour. Highlights: • A novel copper(II) coordination polymer with terepthalate dianion was grown in an aqueous solution. • The single crystal growth temperature was 25 °C for period of two weeks. • The magnetic property of the complex was studied using SQUID. • The complex showed antiferromagnetic properties.
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Climate change alters slug abundance but not herbivory in a temperate grassland
Climate change will significantly impact the world’s ecosystems, in part by altering species interactions and ecological processes, such as herbivory and plant community dynamics, which may impact forage quality and ecosystem production. Yet relatively few field experimental manipulations assessing all of these parameters have been performed to date. To help fill this knowledge gap, we evaluated the effects of increased temperature (+3°C day and night, year-round) and precipitation (+30% of mean annual rainfall) on slug herbivory and abundance and plant community dynamics biweekly in a pasture located in central Kentucky, U.S.A. Warming increased slug abundance once during the winter, likely due to improving conditions for foraging, whereas warming reduced slug abundance at times in late spring, mid-summer, and early fall (from 62–95% reduction depending on month). We found that warming and increased precipitation did not significantly modify slug herbivory at our site, despite altering slug abundance and affecting plant community composition and forage quality. Climate change will alter seasonal patterns of slug abundance through both direct effects on slug biology and indirect effects mediated by changes in the plant community, suggesting that pasture management practices may have to adapt.
59 BASIC BIOLOGICAL SCIENCES↗
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↗
Fluctuations and massive separation in three-dimensional shock-wave/boundary-layer interactions
Shock-wave unsteadiness was observed in rapidly compressed supersonic turbulent boundary layer flows with significant separation. A Mach 2.85 shock-wave/turbulent boundary layer flow was set up over a series of cylinder-flare bodies in the High Reynolds Number Channel 1. The transition from fully attached to fully separated flow was studied using axisymmetric flares with increasing compression angles. In the second phase, the 30 deg flare was inclined relative to the cylinder axis, so that the effect on a separated flow of increasing 3 dimensionality could be observed. Two 3-D separated cases are examined. A simple conditional sampling technique is applied to the data to group them according to an associated shock position. Mean velocities and turbulent kinetic energies, computed from the conditionally samples data, are compared to those from the unsorted data and to computed values. Three basic questions were addressed: can conditional sampling be used to provide snapshots of the flow; are averaged turbulence quantities dominated by the bimodal nature of the interaction; and is the shock unsteadiness really important to computational accuracy.
Kussoy, M. I.↗
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↗
Fluctuations and massive separation in three-dimensional shock-wave/boundary-layer interactions
Shock-wave unsteadiness was observed in rapidly compressed supersonic turbulent boundary layer flows with significant separation. A Mach 2.85 shock-wave/turbulent boundary layer flow was set up over a series of cylinder-flare bodies in the High Reynolds Number Channel 1. The transition from fully attached to fully separated flow was studied using axisymmetric flares with increasing compression angles. In the second phase, the 30-deg flare was inclined relative to the cylinder axis, so that the effect on a separated flow of increasing three-dimensionality could be observed. Two 3-D separated cases are examined. A simple conditional sampling technique is applied to the data to group them according to an associated shock position. Mean velocities and turbulent kinetic energies, computed from the conditionally sampled data, are compared to those from the unsorted data and to computed values. Three basic questions were addressed: can conditional sampling be used to provide snapshots of the flow; are averaged turbulence quantities dominated by the bimodal nature of the interaction; and is the shock unsteadiness really important to computational accuracy.
Kussoy, M. I.↗
ISS Microgravity Research Payload Training Methodology
The NASA Microgravity Research Discipline has multiple categories of science payloads that are being planned and currently under development to operate on various ISS on-orbit increments. The current program includes six subdisciplines; Materials Science, Fluids Physics, Combustion Science, Fundamental Physics, Cellular Biology and Macromolecular Biotechnology. All of these experiment payloads will require the astronaut various degrees of crew interaction and science observation. With the current programs planning to build various facility class science racks, the crew will need to be trained on basic core operations as well as science background. In addition, many disciplines will use the Express Rack and the Microgravity Science Glovebox (MSG) to utilize the accommodations provided by these facilities for smaller and less complex type hardware. The Microgravity disciplines will be responsible to have a training program designed to maximize the experiment and hardware throughput as well as being prepared for various contingencies both with anomalies as well as unexpected experiment observations. The crewmembers will need various levels of training from simple tasks as power on and activate to extensive training on hardware mode change out to observing the cell growth of various types of tissue cultures. Sample replacement will be required for furnaces and combustion type modules. The Fundamental Physics program will need crew EVA support to provide module change out of experiment. Training will take place various research centers and hardware development locations. It is expected that onboard training through various methods and video/digital technology as well as limited telecommunication interaction. Since hardware will be designed to operate from a few weeks to multiple research increments, flexibility must be planned in the training approach and procedure skills to optimize the output as well as the equipment maintainability. Early increment lessons learned will be addressed.
Schlagheck, Ronald↗
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.
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