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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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At least 343 records · Page 19
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Structure of Copper–Cobalt Surface Alloys in Equilibrium with Carbon Monoxide Gas

Here, we studied the structure of the copper–cobalt (CuCo) surface alloy, formed by Co deposition on Cu(110), in dynamic equilibrium with CO. Using scanning tunneling microscopy (STM), we found that, in vacuum at room temperature and at low Co coverage, clusters of a few Co atoms substituting Cu atoms form at the surface. At CO pressures in the Torr range, we found that up to 2.5 CO molecules can bind on a single Co atom, in carbonyl-like configurations. Based on high-resolution STM images, together with density functional theory calculations, we determined the most stable CuCo cluster structures formed with bound CO. Such carbonyl-like formation manifests in shifts in the binding energy of the Co core-level peaks in X-ray photoelectron spectra, as well as shifts in the vibrational modes of adsorbed CO in infrared reflection absorption spectra. The multiple CO adsorption on a Co site weakens the Co–CO bond and thus reduces the C–O bond scission probability. Our results may explain the different product distribution, including higher selectivity toward alcohol formation, when bimetallic CuCo catalysts are used compared to pure Co.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Crystal structure of the Arabidopsis SPIRAL2 C-terminal domain reveals a p80-Katanin-like domain

Epidermal cells of dark-grown plant seedlings reorient their cortical microtubule arrays in response to blue light from a net lateral orientation to a net longitudinal orientation with respect to the long axis of cells. The molecular mechanism underlying this microtubule array reorientation involves katanin, a microtubule severing enzyme, and a plant-specific microtubule associated protein called SPIRAL2. Katanin preferentially severs longitudinal microtubules, generating seeds that amplify the longitudinal array. Upon severing, SPIRAL2 binds nascent microtubule minus ends and limits their dynamics, thereby stabilizing the longitudinal array while the lateral array undergoes net depolymerization. To date, no experimental structural information is available for SPIRAL2 to help inform its mechanism. To gain insight into SPIRAL2 structure and function, we determined a 1.8 Å resolution crystal structure of the Arabidopsis thaliana SPIRAL2 C-terminal domain. The domain is composed of seven core α-helices, arranged in an α-solenoid. Amino-acid sequence conservation maps primarily to one face of the domain involving helices α1, α3, α5, and an extended loop, the α6-α7 loop. The domain fold is similar to, yet structurally distinct from the C-terminal domain of Ge-1 (an mRNA decapping complex factor involved in P-body localization) and, surprisingly, the C-terminal domain of the katanin p80 regulatory subunit. The katanin p80 C-terminal domain heterodimerizes with the MIT domain of the katanin p60 catalytic subunit, and in metazoans, binds the microtubule minus-end factors CAMSAP3 and ASPM. Structural analysis predicts that SPIRAL2 does not engage katanin p60 in a mode homologous to katanin p80. The SPIRAL2 structure highlights an interesting evolutionary convergence of domain architecture and microtubule minus-end localization between SPIRAL2 and katanin complexes, and establishes a foundation upon which structure-function analysis can be conducted to elucidate the role of this domain in the regulation of plant microtubule arrays.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Venado acceptance: results and tips [Slides]

Nvidia compiler support is not available through cray-mpich/compiler wrapper interface. Adjust CMAKE files to use the correct COMPILER_ID in conditionals and explicit variables to package flags. Use pinned host memory in cray-libsci_acc and cublasXt calls. Set a large blockDim for cublasXt calls. Try MPS and/or explicit numactl binding if performance is lackluster. Use CRAY_MALLOPT_OFF=1 if unexpected OOM errors appear using cce. Use MPICH_SMP_SINGLE_COPY_MODE=CMA for xpmem issues. Use MPICH_OPT_THREAD_SYNC=0 for MPI_THREAD issues. Poor CUDA-aware MPI performance remains an issue.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

Vaccine-elicited receptor-binding site antibodies neutralize two New World hemorrhagic fever arenaviruses

While five arenaviruses cause human hemorrhagic fevers in the Western Hemisphere, only Junin virus (JUNV) has a vaccine. The GP1 subunit of their envelope glycoprotein binds transferrin receptor 1 (TfR1) using a surface that substantially varies in sequence among the viruses. As such, receptor-mimicking antibodies described to date are type-specific and lack the usual breadth associated with this mode of neutralization. Here we isolate, from the blood of a recipient of the live attenuated JUNV vaccine, two antibodies that cross-neutralize Machupo virus with varying efficiency. Structures of GP1–Fab complexes explain the basis for efficient cross-neutralization, which involves avoiding receptor mimicry and targeting a conserved epitope within the receptor-binding site (RBS). The viral RBS, despite its extensive sequence diversity, is therefore a target for cross-reactive antibodies with activity against New World arenaviruses of public health concern.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Abnormal Cannabidiol Modulates Vitamin A Metabolism by Acting as a Competitive Inhibitor of CRBP1

Cellular retinol-binding proteins (CRBPs) facilitate the uptake and intracellular transport of vitamin A. They integrate retinoid metabolism, playing an important role in regulating the synthesis of bioactive vitamin A metabolites. Thus, CRBPs constitute potential pharmacological targets to modulate cellular retinoid status that in turn may have applications in the treatment of certain immunological, metabolic, and ocular disorders. Here in this paper we identify abnormal cannabidiol (abn-CBD) as a nonretinoid inhibitor of cellular retinol-binding protein 1 (CRBP1). X-ray crystal structures of CRBP1 in complex with abn-CBD and its derivatives revealed a distinctive mode of protein–ligand interaction and provided a molecular basis for the high affinity and selectivity of this compound. We demonstrated that abn-CBD modulates the flux of retinoids via the retinoid cycle in vivo. Furthermore, the biological activity of abn-CBD was evidenced by its ability to protect against light-induced retinal damage in Balb/cJ mice. Altogether, our findings indicate that targeting selected CRBPs with a small-molecule inhibitor can potentially lead to the development of new therapeutic agents to counteract diseases with etiologies involving imbalance in retinoid metabolism or signaling.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Structural basis for the inability of chloramphenicol to inhibit peptide bond formation in the presence of A-site glycine

Ribosome serves as a universal molecular machine capable of synthesis of all the proteins in a cell. Small-molecule inhibitors, such as ribosome-targeting antibiotics, can compromise the catalytic versatility of the ribosome in a context-dependent fashion, preventing transpeptidation only between particular combinations of substrates. Classic peptidyl transferase center inhibitor chloramphenicol (CHL) fails to inhibit transpeptidation reaction when the incoming A site acceptor substrate is glycine, and the molecular basis for this phenomenon is unknown. Here, we present a set of high-resolution X-ray crystal structures that explain why CHL is unable to inhibit peptide bond formation between the incoming glycyl-tRNA and a nascent peptide that otherwise is conducive to the drug action. Our structures reveal that fully accommodated glycine residue can co-exist in the A site with the ribosome-bound CHL. Moreover, binding of CHL to a ribosome complex carrying glycyl-tRNA does not affect the positions of the reacting substrates, leaving the peptide bond formation reaction unperturbed. These data exemplify how small-molecule inhibitors can reshape the A-site amino acid binding pocket rendering it permissive only for specific amino acid residues and rejective for the other substrates extending our detailed understanding of the modes of action of ribosomal antibiotics.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1999

Developmental regulation of the gene for chimeric calcium/calmodulin-dependent protein kinase in anthers

Chimeric Ca(2+)/calmodulin-dependent protein kinase (CCaMK) was cloned from developing anthers of lily (Lilium longiflorum Thumb. cv. Nellie White) and tobacco (Nicotiana tabacum L. cv. Xanthi). Previous biochemical characterization and structure/function studies had revealed that CCaMK has dual modes of regulation by Ca(2+) and Ca(2+)/calmodulin. The unique structural features of CCaMK include a catalytic domain, a calmodulin-binding domain, and a neural visinin-like Ca(2+)-binding domain. The existence of these three features in a single polypeptide distinguishes it from other kinases. Western analysis revealed that CCaMK is expressed in a stage-specific manner in developing anthers. Expression of CCaMK was first detected in pollen mother cells and continued to increase, reaching a peak around the tetrad stage of meiosis. Following microsporogenesis, CCaMK expression rapidly decreased and at later stages of microspore development, no expression was detected. A tobacco genomic clone of CCaMK was isolated and transgenic tobacco plants were produced carrying the CCaMK promoter fused to the beta-glucuronidase reporter gene. Both CCaMK mRNA and protein were detected in the pollen sac and their localizations were restricted to the pollen mother cells and tapetal cells. Consistent results showing a stage-specific expression pattern were obtained by beta-glucuronidase analysis, in-situ hybridization and immunolocalization. The stage- and tissue-specific appearance of CCaMK in anthers suggests that it could play a role in sensing transient changes in free Ca(2+) concentration in target cells, thereby controlling developmental events in the anther.

NASA Discipline Plant Biology↗
DOE OSTI2021

A Novel Mode of Photoprotection Mediated by a Cysteine Residue in the Chlorophyll Protein IsiA

Oxygenic photosynthetic organisms have evolved a multitude of mechanisms for protection against high-light stress. IsiA, a chlorophyll a-binding cyanobacterial protein, serves as an accessory antenna complex for photosystem I. Intriguingly, IsiA can also function as an independent pigment protein complex in the thylakoid membrane and facilitate the dissipation of excess energy, providing photoprotection. The molecular basis of the IsiA-mediated excitation quenching mechanism remains poorly understood. In this study, we demonstrate that IsiA uses a novel cysteine-mediated process to quench excitation energy. The single cysteine in IsiA in the cyanobacterium Synechocystis sp. strain PCC 6803 was converted to a valine. Ultrafast fluorescence spectroscopic analysis showed that this single change abolishes the excitation energy quenching ability of IsiA, thus providing direct evidence of the crucial role of this cysteine residue in energy dissipation from excited chlorophylls. Under stress conditions, the mutant cells exhibited enhanced light sensitivity, indicating that the cysteine-mediated quenching process is critically important for photoprotection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Membrane association of monotopic phosphoglycosyl transferase underpins function

Polyprenol phosphate phosphoglycosyl transferases (PGTs) catalyze the first membrane-committed step in assembly of essential glycoconjugates. Currently there is no structure–function information to describe how monotopic PGTs coordinate the reaction between membrane-embedded and soluble substrates. We describe the structure and mode of membrane association of PglC, a PGT from Campylobacter concisus. The structure reveals a unique architecture, provides mechanistic insight and identifies ligand-binding determinants for PglC and the monotopic PGT superfamily.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Emulating 2D Materials with Magnons

Spin waves (magnons) in two-dimensional (2D) materials have received increasing interest due to their unique states and potential for tunability. However, many interesting features of these systems, including Dirac points and topological states, occur at high frequencies, where experimental probes are limited. Here, we study a crystal formed by patterning a hexagonal array of holes in a perpendicularly magnetized thin film. Through simulation, we find that the magnonic band structure imitates that of graphene, but additionally has some kagomelike character and includes a few flat bands. Surprisingly, its nature can be understood using a nine-band tight-binding Hamiltonian. This clear analogy to 2D materials enables band-gap engineering in 2D, topological magnons along 1D phase boundaries, and spectrally isolated modes at 0D point defects. Interestingly, the 1D phase boundaries allow access to the valley degree of freedom through a magnonic analog of the quantum valley Hall insulator. These approaches can be extended to other magnonic systems, but are potentially more general due to the simplicity of the model, which resembles existing results from electron, phonon, photon, and cold-atom systems. This finding brings the physics of spin waves in 2D materials to more experimentally accessible scales, augments it, and outlines a few principles for controlling magnonic states.

Ferrimagnets↗
DOE OSTI2018

Crystal structure, Raman spectra, infrared spectra and microwave dielectric properties of Li2Mg3Ti1-X(Mg1/3Ta2/3)XO6 (0 ≤ x ≤ 0.2) solid solution ceramics

Highlights: • Microwave properties of ε{sub r} = 14.70, Q·f = 200,600 GHz and τ{sub f} = −11.83 ppm/°C were obtained. • A small amount of (Mg{sub 1/3}Ta{sub 2/3}){sup 4+} can obviously improve properties. • Rietveld refinement and spectra were used to analyze properties. • Relationships between intrinsic parameters and properties were established. - Abstract: Li{sub 2}Mg{sub 3}Ti{sub 1-X}(Mg{sub 1/3}Ta{sub 2/3}){sub X}O{sub 6} (x = 0.00, 0.05, 0.10, 0.15, 0.20) solid solution ceramics were prepared by the conventional solid-state reaction method. Rietveld refinements, Raman spectra, infrared spectra, polarizability and bond energy were used to research the changes of microwave dielectric properties of these solid solutions. With the increase of x values from 0 to 0.2, dielectric constants (ε{sub r}) gradually increased, which could be explained by the variations of the polarizability, infrared resonant modes and Raman vibration modes. The variations of the quality factor (Q·f) could be explained by the changes of the bond valences. The temperature coefficient of resonant frequency (τ{sub ƒ}) correlated with the bond energy of TiO bonds. A small quantity of (Mg{sub 1/3}Ta{sub 2/3}){sup 4+} can obviously improve the microwave dielectric properties. Excellent microwave dielectric properties of ε{sub r} = 14.70, Q·f = 200,600 GHz and τ{sub f} = −11.83 ppm/°C were obtained for Li{sub 2}Mg{sub 3}Ti{sub 0.95}(Mg{sub 1/3}Ta{sub 2/3}){sub 0.05}O{sub 6} ceramic sintered at 1550 °C.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Analysis methodology of coherent oscillations in time- and angle-resolved photoemission spectroscopy

Oscillatory signals from coherently excited phonons are regularly observed in ultrafast pump–probe experiments on condensed matter samples. Electron–phonon coupling implies that coherent phonons also modulate the electronic band structure. These oscillations can be probed with energy and momentum resolution using time- and angle-resolved photoemission spectroscopy (trARPES), which reveals the orbital dependence of the electron–phonon coupling for a specific phonon mode. However, a comprehensive analysis remains challenging when multiple coherent phonon modes couple to multiple electronic bands. Complex spectral line shapes due to strong correlations in quantum materials add to this challenge. In this work, we examine how the frequency domain representation of trARPES data facilitates a quantitative analysis of coherent oscillations of the electronic bands. Here, we investigate the frequency domain representation of the photoemission intensity and the first moment of the energy distribution curves. Both quantities provide complementary information and are able to distinguish oscillations of binding energy, linewidth, and intensity. We analyze a representative trARPES dataset of the transition metal dichalcogenide WTe 2 and construct composite spectra, which intuitively illustrate how much each electronic band is affected by a specific phonon mode. We also show how a linearly chirped probe pulse can generate extrinsic artifacts that are distinct from the intrinsic coherent phonon signal.

47 OTHER INSTRUMENTATION↗
DOE OSTI2022

Activating alternative transport modes in a multidrug resistance efflux pump to confer chemical susceptibility

Small multidrug resistance (SMR) transporters contribute to antibiotic resistance through proton-coupled efflux of toxic compounds. Previous biophysical studies of the E. coli SMR transporter EmrE suggest that it should also be able to perform proton/toxin symport or uniport, leading to toxin susceptibility rather than resistance in vivo. Here we show EmrE does confer susceptibility to several previously uncharacterized small-molecule substrates in E. coli, including harmane. In vitro electrophysiology assays demonstrate that harmane binding triggers uncoupled proton flux through EmrE. Assays in E. coli are consistent with EmrE-mediated dissipation of the transmembrane pH gradient as the mechanism underlying the in vivo phenotype of harmane susceptibility. Furthermore, checkerboard assays show this alternative EmrE transport mode can synergize with some existing antibiotics, such as kanamycin. These results demonstrate that it is possible to not just inhibit multidrug efflux, but to activate alternative transport modes detrimental to bacteria, suggesting a strategy to address antibiotic resistance.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Unmasking the Origin of Kinks in the Photoemission Spectra of Cuprate Superconductors

The origin of a ubiquitous bosonic coupling feature in the photoemission spectra of high- T c cuprates, an energy-momentum dispersion “kink” observed at ~70 meV binding energy, remains a two-decade-old mystery. Understanding this phenomenon requires an accurate description of the coupling between the electron and some collective modes. In this work, we report ab initio calculations based on G W perturbation theory and show that correlation-enhanced electron-phonon interaction in cuprates gives rise to the strong kinks, which not only explains quantitatively the observations but provides new understanding of experiments. Our results reveal it is the electron density of states being the predominant factor in determining the doping dependence of the kink size, manifesting the multiband nature of the cuprates, as opposed to the prevalent belief of it being a measure of the mode-coupling strength.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Synthesis and Thermal Oxidation Resistance of Boron-Rich Boron–Carbide Material

A boron-rich boron–carbide material (B4+δC) was synthesized by spark plasma sintering of a ball-milled mixture of high-purity boron powder and graphitic carbon at a pressure of 7 MPa and a temperature of 1930 °C. This high-pressure, high-temperature synthesized material was recovered and characterized by X-ray diffraction, X-ray photoelectron spectroscopy, Raman spectroscopy, Vickers hardness measurements, and thermal oxidation studies. The X-ray diffraction studies revealed a single-phase rhombohedral structure (space group R-3m) with lattice parameters in hexagonal representation as a = 5.609 ± 0.007 Å and c = 12.082 ± 0.02 Å. The experimental lattice parameters result in a value of δ = 0.55, or the composition of the synthesized compound as B4.55C. The high-resolution scans of boron binding energy reveal the existence of a B-C bond at 188.5 eV. Raman spectroscopy reveals the existence of a 386 cm−1 vibrational mode representative of C-B-B linear chain formation due to excess boron in the lattice. The measured Vickers microhardness at a load of 200 gf shows a high hardness value of 33.8 ± 2.3 GPa. Thermal gravimetric studies on B4.55C were conducted at a temperature of 1300 °C in a compressed dry air environment, and its behavior is compared to other high-temperature ceramic materials such as high-entropy transition metal boride. The high neutron absorption cross section, high melting point, high mechanical strength, and thermal oxidation resistance make this material ideal for applications in extreme environments.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Structural Basis of Pan-Ebolavirus Neutralization by a Human Antibody against a Conserved, yet Cryptic Epitope

ABSTRACT Only one naturally occurring human antibody has been described thus far that is capable of potently neutralizing all five ebolaviruses. Here we present two crystal structures of this rare, pan-ebolavirus neutralizing human antibody in complex with Ebola virus and Bundibugyo virus glycoproteins (GPs), respectively. The structures delineate the key protein and glycan contacts for binding that are conserved across the ebolaviruses, explain the antibody’s unique broad specificity and neutralization activity, and reveal the likely mechanism behind a known escape mutation in the fusion loop region of GP2. We found that the epitope of this antibody, ADI-15878, extends along the hydrophobic paddle of the fusion loop and then dips down into a highly conserved pocket beneath the N-terminal tail of GP2, a mode of recognition unlike any other antibody elicited against Ebola virus, and likely critical for its broad activity. The fold of Bundibugyo virus glycoprotein, not previously visualized, is similar to the fold of Ebola virus GP, and ADI-15878 binds to each virus’s GP with a similar strategy and angle of attack. These findings will be useful in deployment of this antibody as a broad-spectrum therapeutic and in the design of immunogens that elicit the desired broadly neutralizing immune response against all members of the ebolavirus genus and filovirus family. IMPORTANCE There are five different members of the Ebolavirus genus. Provision of vaccines and treatments able to protect against any of the five ebolaviruses is an important goal of public health. Antibodies are a desired result of vaccines and can be delivered directly as therapeutics. Most antibodies, however, are effective against only one or two, not all, of these pathogens. Only one human antibody has been thus far described to neutralize all five ebolaviruses, antibody ADI-15878. Here we describe the molecular structure of ADI-15878 bound to the relevant target proteins of Ebola virus and Bundibugyo virus. We explain how it achieves its rare breadth of activity and propose strategies to design improved vaccines capable of eliciting more antibodies like ADI-15878.

West, Brandyn R. (ORCID:0000000213990117)↗
NASA NTRS2005

Mineralized Remains of Morphotypes of Filamentous Cyanobacteria in Carbonaceous Meteorites

The quest for conclusive evidence of microfossils in meteorites has been elusive. One difficulty arises from the fact than many abiotic or inorganic microstructures, mineral grains, and coating artifacts can mimic the smaller representatives of the microbial world that possess very simple morphologies (unicellular cocci or bacilli). However, there exist a wide variety of large, filamentous trichomic prokaryotic microorganisms (cyanobacteria and sulfur bacteria) with sufficiently well known and complex morphologies that they can be recognized and are known to be of unquestionable biogenic origin. The taphonomic modes of fossilization and their of their life habits and processes frequently result in distinctive chemical biosignatures associated with carbonization, silicification, calcification, phosphatization and metal-binding properties of their cell-walls, trichomes, sheaths and extracellular polymeric substances (EPS). Strong differences of mineral concentrations in closely associated and visibly differentiated cellular microstructures provide strong evidence of biogenicity. This evidence is further enhanced by the detection of recognizable and distinct microstructures (e.g., uniseriate or multiseriate filaments, trichomes, sheaths, cells of proper sizes and size distributions) and growth characteristics (e.g., basal or apical cells, true or false branching of trichomes, tapered or uniform filaments, robust or thin sheaths) and reproductive and nitrogen fixation habits (e.g., baeocytes, hormogonia, akinetes and heterocysts), Microfossils of cyanobacteria and cyanobacterial mats and stromatolites have been recognized a described from many of the most ancient rocks on Earth. The crucial problem lies in developing valid protocols and methodologies for establishing that the putative microfossils are truly indigenous and not merely recent microbial contaminants. During the past several years, we have conducted Field Emission Scanning Electron Microscopy (FESEM) investigations of freshly fractured interior surfaces of carbonaceous meteorites, terrestrial rocks, and recent microbial extremophiles and filamentous cyanobacteria. These studies have resulted in the detection in a several carbonaceous meteorites of the mineralized remains of a wide variety of complex filamentous trichomic microorganisms. These embedded forms are consistent in size and microstructure with well-preserved morphotypes of mat- forming filamentous trichomic cyanobacteria and the degraded remains of microfibrils of cyanobacterial sheaths. We present the results of comparative imaging studies and EDAX elemental analyses of recent cyanobacteria (e.g. Calothrix, Oscillatoria, and Lyngbya) that are similar in size, morphology and microstructure to morphotypes found embedded in meteorites. EDAX elemental studies reveal that forms found in carbonaceous meteorites often have highly carbonized sheaths in close association with permineralized filaments, trichomes and microbial cells. Ratios of critical bioelements (C:O, C:N, C:P, and C:S) reveal dramatic differences between microfossils in Earth rocks and meteorites and in filaments, trichomes, hormogonia, and cells of recent cyanobacteria.

Hoover, Richard B.↗
DOE OSTI2021

A conformation-selective monoclonal antibody against a small molecule-stabilised signalling-deficient form of TNF

We have recently described the development of a series of small-molecule inhibitors of human tumour necrosis factor (TNF) that stabilise an open, asymmetric, signalling-deficient form of the soluble TNF trimer. Here, we describe the generation, characterisation, and utility of a monoclonal antibody that selectively binds with high affinity to the asymmetric TNF trimer–small molecule complex. The antibody helps to define the molecular dynamics of the apo TNF trimer, reveals the mode of action and specificity of the small molecule inhibitors, acts as a chaperone in solving the human TNF–TNFR1 complex crystal structure, and facilitates the measurement of small molecule target occupancy in complex biological samples. We believe this work defines a role for monoclonal antibodies as tools to facilitate the discovery and development of small-molecule inhibitors of protein–protein interactions.

59 BASIC BIOLOGICAL SCIENCES↗