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At least 721 records · Page 40

Potent HIV‑1 protease inhibitors containing oxabicyclo octanol-derived P2-ligands: Design, synthesis, and X‑ray structural studies of inhibitor-HIV-1 protease complexes

Here, we describe here the design, synthesis, and X-ray structural studies of a new class of HIV-1 protease inhibitors containing 8-oxabicyclo[3.2.1]octanol-derived P2 ligands. We investigated the functional effect of these stereochemically defined fused-poly cyclic ligands on enzyme inhibition and antiviral activity in MT-2 cells. The tricyclic core of 8-oxabicyclo[3.2.1]octan-6-ol is designed to interact with the residues in the S2 subsite of HIV-1 protease. The syntheses of the ligands were carried out using the [5+2]-cycloaddition as the key step. Several inhibitors exhibited potent enzyme inhibitory activity. High resolution room-temperature X-ray structures of inhibitor-bound HIV-1 protease were determined. These structures provided important molecular insights for further design and optimization of inhibitor potency.

60 APPLIED LIFE SCIENCES↗

Exploration of imatinib and nilotinib-derived templates as the P2-Ligand for HIV-1 protease inhibitors: Design, synthesis, protein X-ray structural studies, and biological evaluation

Structure-based design, synthesis, X-ray structural studies, and biological evaluation of a new series of potent HIV-1 protease inhibitors are described. Here, these inhibitors contain various pyridyl-pyrimidine, aryl thiazole or alkylthiazole derivatives as the P2 ligands in combination with darunavir-like hydroxyethylamine sulfonamide isosteres. These heterocyclic ligands are inherent to kinase inhibitor drugs, such as nilotinib and imatinib. These ligands are designed to make hydrogen bonding interactions with the backbone atoms in the S2 subsite of HIV-1 protease. Various benzoic acid derivatives have been synthesized and incorporation of these ligands provided potent inhibitors that exhibited subnanomolar level protease inhibitory activity and low nanomolar level antiviral activity. Two high resolution X-ray structures of inhibitor-bound HIV-1 protease were determined. These structures provided important ligand-binding site interactions for further optimization of this class of protease inhibitors.

60 APPLIED LIFE SCIENCES↗

Structure-based decoupling of the pro- and anti-inflammatory functions of interleukin-10

Interleukin-10 (IL-10) is an immunoregulatory cytokine with both anti-inflammatory and immunostimulatory properties and is frequently dysregulated in disease. We used a structure-based approach to deconvolute IL-10 pleiotropy by determining the structure of the IL-10 receptor (IL-10R) complex by cryo–electron microscopy at a resolution of 3.5 angstroms. The hexameric structure shows how IL-10 and IL-10Rα form a composite surface to engage the shared signaling receptor IL-10Rβ, enabling the design of partial agonists. IL-10 variants with a range of IL-10Rβ binding strengths uncovered substantial differences in response thresholds across immune cell populations, providing a means of manipulating IL-10 cell type selectivity. Some variants displayed myeloid-biased activity by suppressing macrophage activation without stimulating inflammatory CD8 + T cells, thereby uncoupling the major opposing functions of IL-10. These results provide a mechanistic blueprint for tuning the pleiotropic actions of IL-10.

60 APPLIED LIFE SCIENCES↗

Flight and Analytical Methods for Determining the Coupled Vibration Response of Tandem Helicopters

Chapter one presents a discussion of flight-test and analysis methods for some selected helicopter vibration studies. The use of a mechanical shaker in flight to determine the structural response is reported. A method for the analytical determination of the natural coupled frequencies and mode shapes of vibrations in the vertical plane of tandem helicopters is presented in Chapter two. The coupled mode shapes and frequencies are then used to calculate the response of the helicopter to applied oscillating forces.

Yeates, John E , Jr↗

Alabama NASA EPSCoR Preparation Grant Program: Grant No. NCC5-391

The funded research projects under the Experimental Program to Stimulate Cooperative Research (EPSCoR) grant program and the student fellowship awards are summarized in this report. The projects include: 1) Crystallization of Dehydratase/DcoH: A Target in Lung Disease; 2) Measuring Velocity Profiles in Liquid Metals using an Ultrasonic Doppler Velocimeter; 3) Synthesis, Structure, and Properties of New Thermoelectric Materials; 4) Computational Determination of Structures and Reactivity of Phenol-Formaldehyde Resins; 5) Synthesis of Microbial Polyesters in the NASA Bioreactor; 6) Visualization of Flow-Fields in Magnetocombustion; 7) Synthesis of Fluorescent Saccharide Derivatives. The student fellowship awards include: 1) Distributed Fusion of Satellite Images; 2) Study of the Relationship between Urban Development, Local Climate, and Water Quality for the Atlanta, Georgia Metrop; 3) Computer Simulation of the Effectiveness of a Spring-Loaded Exercise Device.

Gregory, John C.↗

Evolving data standards for cryo-EM structures

Electron cryo-microscopy (cryo-EM) is increasingly being used to determine 3D structures of a broad spectrum of biological specimens from molecules to cells. Anticipating this progress in the early 2000s, an international collaboration of scientists with expertise in both cryo-EM and structure data archiving was established (EMDataResource, previously known as EMDataBank). The major goals of the collaboration have been twofold: to develop the necessary infrastructure for archiving cryo-EM-derived density maps and models, and to promote development of cryo-EM structure validation standards. We describe how cryo-EM data archiving and validation have been developed and jointly coordinated for the Electron Microscopy Data Bank and Protein Data Bank archives over the past two decades, as well as the impact of evolving technology on data standards. Just as for X-ray crystallography and nuclear magnetic resonance, engaging the scientific community via workshops and challenging activities has played a central role in developing recommendations and requirements for the cryo-EM structure data archives.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The Reactivity and Structural Dynamics of Supported Metal Nanoclusters Using Electron Microscopy, in-situ X-Ray Spectroscopy, Electronic Structure Theories, and Molecular Dynamics Simulations

This research will provide new methods to determine the structures and compositions of heterogeneous catalysts as they exist in reaction conditions. The new tools will make it possible to understand how extremely small material structures—ones in a size range spanning from single atoms to larger polyatomic clusters—make it possible to carry out highly selective chemical transformations required to synthesize useful materials as well as for efficient energy production and utilization. The tools will make it possible to see how the atomic structures of catalytic materials evolve over time under the conditions of their use, and in this way provide understandings to guide the design of new energy-efficient catalysts. The work will make it possible to answer long standing questions that include the following. How does catalyst structure help guide molecules along specific reaction pathways? What are the important intermediates involved in these transformations? How do the structures and reactivity of catalytic materials, as well as the chemistry of their interfaces, vary with reaction conditions? Is it possible to develop new catalytic materials using new knowledge of the active structures and reaction mechanisms? The work will provide heretofore unavailable experimental tools that can be applied in advanced programs of research addressing such questions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Crystal Structure of Moganite and Its Anisotropic Atomic Displacement Parameters Determined by Synchrotron X-ray Diffraction and X-ray/Neutron Pair Distribution Function Analyses

The crystal structure of moganite from the Mogán formation on Gran Canaria has been re-investigated using high-resolution synchrotron X-ray diffraction (XRD) and X-ray/neutron pair distribution function (PDF) analyses. Our study for the first time reports the anisotropic atomic displacement parameters (ADPs) of a natural moganite. Rietveld analysis of synchrotron XRD data determined the crystal structure of moganite with the space group I2/a. The refined unit-cell parameters are a = 8.7363(8), b = 4.8688(5), c = 10.7203(9) Å, and β = 90.212(4)°. The ADPs of Si and O in moganite were obtained from X-ray and neutron PDF analyses. The shapes and orientations of the anisotropic ellipsoids determined from X-ray and neutron measurements are similar. The anisotropic ellipsoids for O extend along planes perpendicular to the Si-Si axis of corner-sharing SiO4 tetrahedra, suggesting precession-like movement. Neutron PDF result confirms the occurrence of OH over some of the tetrahedral sites. We postulate that moganite nanomineral is stable with respect to quartz in hypersaline water. The ADPs of moganite show a similar trend as those of quartz determined by single-crystal XRD. In short, the combined methods can provide high-quality structural parameters of moganite nanomineral, including its ADPs and extra OH position at the surface. This approach can be used as an alternative means for solving the structures of crystals that are not large enough for single-crystal XRD measurements, such as fine-grained and nanocrystalline minerals formed in various geological environments.

58 GEOSCIENCES↗

Middeck Active Control Experiment (MACE), phase A

A rationale to determine which structural experiments are sufficient to verify the design of structures employing Controlled Structures Technology was derived. A survey of proposed NASA missions was undertaken to identify candidate test articles for use in the Middeck Active Control Experiment (MACE). The survey revealed that potential test articles could be classified into one of three roles: development, demonstration, and qualification, depending on the maturity of the technology and the mission the structure must fulfill. A set of criteria was derived that allowed determination of which role a potential test article must fulfill. A review of the capabilities and limitations of the STS middeck was conducted. A reference design for the MACE test article was presented. Computing requirements for running typical closed-loop controllers was determined, and various computer configurations were studied. The various components required to manufacture the structure were identified. A management plan was established for the remainder of the program experiment development, flight and ground systems development, and integration to the carrier. Procedures for configuration control, fiscal control, and safety, reliabilty, and quality assurance were developed.

Crawley, Edward F.↗

Structural interaction with control systems

A monograph which assesses the state of the art of space vehicle design and development is presented. The monograph presents criteria and recommended practices for determining the structural data and a mathematical structural model of the vehicle needed for accurate prediction of structure and control-system interaction; for design to minimize undesirable interactions between the structure and the control system; and for determining techniques to achieve the maximum desirable interactions and associated structural design benefits. All space vehicles are treated, including launch vehicles, spacecraft, and entry vehicles. Important structural characteristics which affect the structural model used for structural and control-system interaction analysis are given.

Noll, R. B.↗

Structurally Constrained Evolutionary Algorithm for the Discovery and Design of Metastable Phases

Metastable materials are abundant in nature and technology, showcasing remarkable properties that inspire innovative materials design. However, traditional crystal structure prediction methods, which rely solely on energetic factors to determine a structure’s fitness, are not suitable for predicting the vast number of potentially synthesizable phases that represent a local minimum corresponding to a state in thermodynamic equilibrium. Here, we present a new approach for the prediction of metastable phases with specific structural features, and interface this method with the XTALOPT evolutionary algorithm. Our method relies on structural features that include the local crystalline order (e.g., the coordination number or chemical environment), and symmetry (e.g., Bravais lattice and space group) to filter the breeding pool of an evolutionary crystal structure search. The effectiveness of this approach is benchmarked on three known metastable systems: XeN 8 , with a two-dimensional polymeric nitrogen sublattice, brookite TiO 2 , and a high pressure BaH 4 phase that was recently characterized. Additionally, a newly predicted metastable melaminate salt, P1¯WC 3 N 6 , was found to possess an energy that is lower than two phases proposed in a recent computational study. Here, the method presented here could help in identifying the structures of compounds that have already been synthesized, and developing new synthesis targets with desired properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Role of Postdeposition Thermal Annealing on Intracrystallite and Intercrystallite Structuring and Charge Transport in Poly(3-hexylthiophene)

The performance of electronic devices comprising conjugated polymers as the active layer depends not only on the intrinsic characteristics of the materials but also on the details of the extrinsic processing conditions. Here, we examine the effect of postdeposition thermal treatments on the microstructure of poly(3-hexylthiophene) (P3HT) thin films and its impact on their electrical properties. Unsurprisingly, we find thermal annealing of P3HT thin films to generally increase their crystallinity and crystallite coherence length while retaining the same crystal structure. Despite such favorable structural improvements of the polymer active layers, however, thermal annealing at high temperatures can lead to a net reduction in the mobility of transistors, implicating structural changes in the intercrystallite amorphous regions of these semicrystalline active layers take place on annealing, and the simplistic picture that crystallinity governs charge transport is not always valid. Our results instead suggest tie-chain pullout, which occurs during crystal growth and perfection upon thermal annealing to govern charge transport, particularly in low-molecular-weight systems in which the tie-chain fraction is low. By demonstrating the interplay between intracrystallite and intercrystallite structuring in determining the macroscopic charge transport, we shed light on how structural evolution and charge-transport properties of nominally the same polymer can vary depending on the details of processing.

36 MATERIALS SCIENCE↗

How μ-opioid receptor recognizes fentanyl

Abstract Roughly half of the drug overdose-related deaths in the United States are related to synthetic opioids represented by fentanyl which is a potent agonist of mu-opioid receptor (mOR). In recent years, X-ray crystal structures of mOR in complex with morphine derivatives have been determined; however, structural basis of mOR activation by fentanyl-like opioids remains lacking. Exploiting the X-ray structure of BU72-bound mOR and several molecular simulation techniques, we elucidated the detailed binding mechanism of fentanyl. Surprisingly, in addition to the salt-bridge binding mode common to morphinan opiates, fentanyl can move deeper and form a stable hydrogen bond with the conserved His297 6.52 , which has been suggested to modulate mOR’s ligand affinity and pH dependence by previous mutagenesis experiments. Intriguingly, this secondary binding mode is only accessible when His297 6.52 adopts a neutral HID tautomer. Alternative binding modes may represent a general mechanism in G protein-coupled receptor-ligand recognition.

60 APPLIED LIFE SCIENCES↗

Hydrophobic interactions dominate the recognition of a KRAS G12V neoantigen

Specificity remains a major challenge to current therapeutic strategies for cancer. Mutation associated neoantigens (MANAs) are products of genetic alterations, making them highly specific therapeutic targets. MANAs are HLA-presented (pHLA) peptides derived from intracellular mutant proteins that are otherwise inaccessible to antibody-based therapeutics. Here, we describe the cryo-EM structure of an antibody-MANA pHLA complex. Specifically, we determine a TCR mimic (TCRm) antibody bound to its MANA target, the KRAS G12V peptide presented by HLA-A*03:01. Hydrophobic residues appear to account for the specificity of the mutant G12V residue. We also determine the structure of the wild-type G12 peptide bound to HLA-A*03:01, using X-ray crystallography. Based on these structures, we perform screens to validate the key residues required for peptide specificity. These experiments led us to a model for discrimination between the mutant and the wild-type peptides presented on HLA-A*03:01 based exclusively on hydrophobic interactions.

36 MATERIALS SCIENCE↗

Improving energy yield in photovoltaic modules with photonic structures

When installed outdoors, Si solar cells typically operate 20 – 30 K above ambient conditions. These elevated operating temperatures lead to diminished performance, reducing efficiency by ~0.4%/K for crystalline Si cells and decreasing module lifetime. Since much of the elevated temperature of the modules derives from parasitic absorption of sub-bandgap sunlight by the contacts, encapsulants, or other materials, reflectors that remove the sub-bandgap radiation from the module before it is absorbed promise to reduce the operating temperature. However, there are many competing strategies to reject this light: selective reflectors could be integrated into the outer module glass, at the textured Si-encapsulant interface, or on the rear. Furthermore, many of these approaches are complex and expensive to fabricate. The issue of heating can be even more critical in bifacial modules: high fractions of rear irradiance can lead to higher operating temperatures. Prior to this project, relatively little was known about the optical strategies for temperature reduction in bifacial modules. The goal of this project was to quantitatively assess optical strategies for improving the energy yield via a combination of improved anti-reflection and sub-bandgap light rejection. We studied two complementary concepts: the performance of ideal structures to determine the upper limits to performance, and low-complexity structures made from standard materials as cost-effective implementations. We also studied the performance of these reflectors in different types of modules, including Al BSF, PERC, and bifacial. Here we build from our prior accomplishments in developing mirror optimization techniques, and make use of simulation methods that accurately capture the optical properties of the modules throughout the visible and near-infrared spectrum. We connect these optical properties to energy yield under realistic, outdoor conditions. We also experimentally fabricated mirrors, incorporated them into mini-modules, and performed outdoor testing of performance at NREL. We found definitively that spectrally-selective mirrors on the outside of the module cover glass offer the best performance, both under ideal conditions and for realistic, low- complexity mirrors. Mirrors at the Si cell/encapsulant interface are limited by the multiple reflections needed to remove sub-bandgap light. Mirrors at the cell surface and mirrors on the rear also cannot remove all the sub-bandgap light, since parasitic absorption also occurs in the cover glass, encapsulant, and front contacts, depending on the module configuration. Also, cell texturing places higher demands on any cell-surface mirror because multiple interactions with the mirror are required to reject sub bandgap light which compounds losses. For bifacial modules, mirrors on the back do provide additional cooling and energy yield improvements, and the mirrors can have the same structure. In the monofacial case up to 3.3K of cooling is possible for mirrors on the front, compared to 2.2K at the cell surface and 1.2K at the rear. For bifacial modules, up to 2.4K of cooling is possible when mirrors are included at both the front and back. Our realistic designs utilize 4 – 6 layers of common photovoltaic materials such as SiO 2 , TiO 2 , and SiN x , making them more cost effective. Finally, we used our models to study thermal management in bifacial modules with different back lamination materials, finding that glass-glass laminated modules operated hotter than equivalent glass-polymer backsheet modules, due solely to the increased absorption of light incident from the rear of the module. Improving the energy yield by 2%, which is achievable with these realistic designs, would lead to LCOE reductions of $0.03/kWh by 2030. These benefits make photovoltaic panels more accessible to the public and may reduce associated maintenance costs.

14 SOLAR ENERGY↗