Results for “Structure Determination” — Page 59

DOE OSTI2020

A highly conserved cryptic epitope in the receptor binding domains of SARS-CoV-2 and SARS-CoV

Abstract not provided

Yuan, Meng↗

DOE OSTI2022

A human antibody reveals a conserved site on beta-coronavirus spike proteins and confers protection against SARS-CoV-2 infection

Broadly neutralizing antibodies (bnAbs) to coronaviruses (CoVs) are valuable in their own right as prophylactic and therapeutic reagents to treat diverse CoVs and as templates for rational pan-CoV vaccine design. We recently described a bnAb, CC40.8, from a CoV disease 2019 (COVID-19) convalescent donor that exhibits broad reactivity with human β-CoVs. Here, we showed that CC40.8 targets the conserved S2 stem helix region of the CoV spike fusion machinery. We determined a crystal structure of CC40.8 Fab with a SARS-CoV-2 S2 stem peptide at 1.6-Å resolution and found that the peptide adopted a mainly helical structure. Conserved residues in β-CoVs interacted with CC40.8 antibody, thereby providing a molecular basis for its broad reactivity. CC40.8 exhibited in vivo protective efficacy against SARS-CoV-2 challenge in two animal models. In both models, CC40.8-treated animals exhibited less weight loss and reduced lung viral titers compared to controls. Furthermore, we noted that CC40.8-like bnAbs are relatively rare in human COVID-19 infection, and therefore, their elicitation may require rational structure-based vaccine design strategies. Overall, our study describes a target on β-CoV spike proteins for protective antibodies that may facilitate the development of pan–β-CoV vaccines.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Sensor Domain of Histidine Kinase VxrA of Vibrio cholerae : Hairpin-Swapped Dimer and Its Conformational Change

VxrA and VxrB are cognate histidine kinase (HK)-response regulator (RR) pairs of a two-component signaling system (TCS) found in Vibrio cholerae, a bacterial pathogen that causes cholera. The VxrAB TCS positively regulates virulence, the type VI secretion system, biofilm formation, and cell wall homeostasis in V. cholerae, providing protection from environmental stresses and contributing to the transmission and virulence of the pathogen. The VxrA HK has a unique periplasmic sensor domain (SD) and, remarkably, lacks a cytoplasmic linker domain between the second transmembrane helix and the dimerization and histidine phosphotransfer (DHp) domain, indicating that this system may utilize a potentially unique signal sensing and transmission TCS mechanism. Here, we have determined several crystal structures of VxrA-SD and its mutants. These structures reveal a novel structural fold forming an unusual β hairpin-swapped dimer. A conformational change caused by relative rotation of the two monomers in a VxrA-SD dimer could potentially change the association of transmembrane helices and, subsequently, the pairing of cytoplasmic DHp domains. Based on the structural observation, we propose a putative scissor-like closing regulation mechanism for the VxrA HK. IMPORTANCE V. cholerae has a dynamic life cycle, which requires rapid adaptation to changing external conditions. Two-component signal transduction (TCS) systems allow V. cholerae to sense and respond to these environmental changes. The VxrAB TCS positively regulates a number of important V. cholerae phenotypes, including virulence, the type six secretion system, biofilm formation, and cell wall homeostasis. Here, we provide the crystal structures of the VxrA sensor histidine kinase sensing domain and propose a mechanism for signal transduction. The cognate signal for VxrAB remains unknown; however, in this work we couple our structural analysis with functional assessments of key residues to further our understanding of this important TCS.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Hyperon III: $$K^{-}p - \pi \varSigma $$ coupled-channel dynamics in the $$\varLambda (1405)$$ mass region

Abstract Low-energy data on the three charge states in $$\gamma p \rightarrow K^+(\varSigma \pi )$$ γ p → K + ( Σ π ) from CLAS at JLab, on $$K^-p\rightarrow \pi ^0\pi ^0\varLambda $$ K - p → π 0 π 0 Λ and $$\pi ^0\pi ^0\varSigma $$ π 0 π 0 Σ from the Crystal Ball at BNL, bubble chamber data on $$K^-p\rightarrow \pi ^-\pi ^+\pi ^{\pm }\varSigma ^{\mp }$$ K - p → π - π + π ± Σ ∓ , low-energy total cross sections on $$K^-$$ K - induced reactions, and data on the $$K^-p$$ K - p atom are fitted with the BnGa partial-wave-analysis program. We find that the data can be fitted well with just one isoscalar spin-1/2 negative-parity pole, the $$\varLambda (1405)$$ Λ ( 1405 ) , and background contributions. In a fit with one isocsalar state, the $$\varLambda (1405)$$ Λ ( 1405 ) structure can be determined as a dominantly SU(3) singlet state. A fit with two isoscalar singlet states, with imposed properties of the low-mass state, is, however, also not incompatible with data.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2021

Degradation of Platinum-Cobalt Alloy PEMFC Cathode Catalysts in Catalyst-Ionomer Inks

In this paper we report on studies of the effects of catalyst-ionomer ink composition: ionomer equivalent weight (EW), ink solvent, and ink mixing on a commercial PtCo alloy PEMFC cathode catalyst. X-ray absorption spectroscopy (XAS) and wide-angle X-ray scattering (WAXS) are utilized to determine catalyst atomic structure, catalyst crystallite composition, and extent of loss of Co into the ionomer-solvent phase. Three different n-propanol to water weight ratios (7:3, 5:5, and 3:7) and two different ionomers (3 M 800 EW and Nafion 1000 EW) were studied. Cobalt loss from the PtCo particles was found to increase with increasing water content in the inks and to be more extensive for the 800 EW ionomer inks, causing loss of contraction of the PtCo lattice and formation of a Pt shell-PtCo alloy core intraparticle structure.

25 ENERGY STORAGE↗

DOE OSTI2021

Mapathons versus automated feature extraction: a comparative analysis for strengthening immunization microplanning

Background: Social instability and logistical factors like the displacement of vulnerable populations, the difficulty of accessing these populations, and the lack of geographic information for hard-to-reach areas continue to serve as barriers to global essential immunizations (EI). Microplanning, a population-based, healthcare intervention planning method has begun to leverage geographic information system (GIS) technology and geospatial methods to improve the remote identification and mapping of vulnerable populations to ensure inclusion in outreach and immunization services, when feasible. We compare two methods of accomplishing a remote inventory of building locations to assess their accuracy and similarity to currently employed microplan line-lists in the study area. Methods: The outputs of a crowd-sourced digitization effort, or mapathon, were compared to those of a machine-learning algorithm for digitization, referred to as automatic feature extraction (AFE). The following accuracy assessments were employed to determine the performance of each feature generation method: (1) an agreement analysis of the two methods assessed the occurrence of matches across the two outputs, where agreements were labeled as “befriended” and disagreements as “lonely”; (2) true and false positive percentages of each method were calculated in comparison to satellite imagery; (3) counts of features generated from both the mapathon and AFE were statistically compared to the number of features listed in the microplan line-list for the study area; and (4) population estimates for both feature generation method were determined for every structure identified assuming a total of three households per compound, with each household averaging two adults and 5 children. Results: The mapathon and AFE outputs detected 92,713 and 53,150 features, respectively. A higher proportion (30%) of AFE features were befriended compared with befriended mapathon points (28%). The AFE had a higher true positive rate (90.5%) of identifying structures than the mapathon (84.5%). The difference in the average number of features identified per area between the microplan and mapathon points was larger (t = 3.56) than the microplan and AFE (t = -2.09) (alpha = 0.05). Conclusions: Our findings indicate AFE outputs had higher agreement (i.e., befriended), slightly higher likelihood of correctly identifying a structure, and were more similar to the local microplan line-lists than the mapathon outputs. These findings suggest AFE may be more accurate for identifying structures in high-resolution satellite imagery than mapathons. However, they both had their advantages and the ideal method would utilize both methods in tandem.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020