Potent neutralizing nanobodies resist convergent circulating variants of SARS-CoV-2 by targeting novel and conserved epitopes

AbstractThere is an urgent need to develop effective interventions resistant to the evolving variants of SARS-CoV-2. Nanobodies (Nbs) are stable and cost-effective agents that can be delivered by novel aerosolization route to treat SARS-CoV-2 infections efficiently. However, it remains unknown if they possess broadly neutralizing activities against the prevalent circulating strains. We found that potent neutralizing Nbs are highly resistant to the convergent variants of concern that evade a large panel of neutralizing antibodies (Abs) and significantly reduce the activities of convalescent or vaccine-elicited sera. Subsequent determination of 9 high-resolution structures involving 6 potent neutralizing Nbs by cryoelectron microscopy reveals conserved and novel epitopes on virus spike inaccessible to Abs. Systematic structural comparison of neutralizing Abs and Nbs provides critical insights into how Nbs uniquely target the spike to achieve high-affinity and broadly neutralizing activity against the evolving virus. Our study will inform the rational design of novel pan-coronavirus vaccines and therapeutics.

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Potent neutralizing nanobodies resist convergent circulating variants of SARS-CoV-2 by targeting diverse and conserved epitopes

Nature Communications ◽

10.1038/s41467-021-24963-3 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Dapeng Sun ◽

Zhe Sang ◽

Yong Joon Kim ◽

Yufei Xiang ◽

Tomer Cohen ◽

...

Keyword(s):

Receptor Binding ◽

Binding Sites ◽

Neutralizing Antibodies ◽

Rational Design ◽

Function Analysis ◽

Receptor Binding Domain ◽

High Affinity ◽

Activity Structure ◽

Neutralizing Epitopes

AbstractInterventions against variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are urgently needed. Stable and potent nanobodies (Nbs) that target the receptor binding domain (RBD) of SARS-CoV-2 spike are promising therapeutics. However, it is unknown if Nbs broadly neutralize circulating variants. We found that RBD Nbs are highly resistant to variants of concern (VOCs). High-resolution cryoelectron microscopy determination of eight Nb-bound structures reveals multiple potent neutralizing epitopes clustered into three classes: Class I targets ACE2-binding sites and disrupts host receptor binding. Class II binds highly conserved epitopes and retains activity against VOCs and RBDSARS-CoV. Cass III recognizes unique epitopes that are likely inaccessible to antibodies. Systematic comparisons of neutralizing antibodies and Nbs provided insights into how Nbs target the spike to achieve high-affinity and broadly neutralizing activity. Structure-function analysis of Nbs indicates a variety of antiviral mechanisms. Our study may guide the rational design of pan-coronavirus vaccines and therapeutics.

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Presynaptic, high-affinity glutamate uptake in excitatory neuromuscular junctions of the retractor unguis muscle of the locust: determination of the Km value using high resolution autoradiography

Experimental Brain Research ◽

10.1007/bf00237400 ◽

1986 ◽

Vol 62 (1) ◽

pp. 25-28 ◽

Cited By ~ 4

Author(s):

J. van Marle ◽

T. Piek ◽

R. D. Veldsema-Currie

Keyword(s):

High Resolution ◽

Neuromuscular Junctions ◽

Glutamate Uptake ◽

High Affinity ◽

Km Value ◽

High Resolution Autoradiography

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Environmental Soil and Ground Water Assessment Using High Resolution Passive Soil-Gas Samplers - Petrex Method: Methodology and Results of a Case Study Performed in Brazil

Water Science & Technology ◽

10.2166/wst.1994.0403 ◽

1994 ◽

Vol 29 (8) ◽

pp. 161-172 ◽

Cited By ~ 5

Author(s):

D. C. Gomes ◽

M. Alarsa ◽

M. C. Salvador ◽

C. Kupferschmid

Keyword(s):

High Resolution ◽

High Resolution Mass Spectrometry ◽

Cost Effective ◽

Site Investigation ◽

Soil Gas ◽

Environmental Evaluation ◽

Direct Sampling ◽

Selection Of

The PETREX Passive Soil Gas Technique - applied successfully to environmental projects for 10 years - is the ideal primary investigative tool for soil and groundwater contaminations, since it is rapid, easy to apply and covers large areas. It is more sensitive and cost effective than other methods (e.g. active soil gas techniques). Passive collectors combined with high-resolution mass spectrometry permit direct mid reliable identification of over 9,000 volatile (VOCs) and semi-volatile organic compounds (SVOCs). PETREX is capable of providing comprehensive problem delineation during the initial stages of the site investigation, allowing for greater cost effectiveness in the planning of remediation programs and in the selection of appropriate monitoring well locations and other methodologies which may be needed to complete the environmental evaluation. PETREX therefore finds wide use in the investigation of contaminants, in the determination of pollution sources, as well as in audits connected to real estate transactions. This paper describes a case-study developed in Brazil, showing PETREX's usefulness and its correlation with soil and groundwater contamination plumes established from traditional direct sampling methods.

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Artificial Biomimetic Electrochemical Assemblies

Biosensors ◽

10.3390/bios12010044 ◽

2022 ◽

Vol 12 (1) ◽

pp. 44

Author(s):

Tanja Zidarič ◽

Matjaž Finšgar ◽

Uroš Maver ◽

Tina Maver

Keyword(s):

Supramolecular Chemistry ◽

Molecularly Imprinted Polymers ◽

Cost Effective ◽

Molecularly Imprinted ◽

Imprinted Polymers ◽

High Affinity ◽

Sensor Platforms ◽

Gate Effect ◽

Target Analytes

Rapid, selective, and cost-effective detection and determination of clinically relevant biomolecule analytes for a better understanding of biological and physiological functions are becoming increasingly prominent. In this regard, biosensors represent a powerful tool to meet these requirements. Recent decades have seen biosensors gaining popularity due to their ability to design sensor platforms that are selective to determine target analytes. Naturally generated receptor units have a high affinity for their targets, which provides the selectivity of a device. However, such receptors are subject to instability under harsh environmental conditions and have consequently low durability. By applying principles of supramolecular chemistry, molecularly imprinted polymers (MIPs) can successfully replace natural receptors to circumvent these shortcomings. This review summarizes the recent achievements and analytical applications of electrosynthesized MIPs, in particular, for the detection of protein-based biomarkers. The scope of this review also includes the background behind electrochemical readouts and the origin of the gate effect in MIP-based biosensors.

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High-resolution microscopy of twin boundaries in gold

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100126202 ◽

1987 ◽

Vol 45 ◽

pp. 260-261

Author(s):

William Krakow ◽

David A. Smith

Keyword(s):

High Resolution ◽

Specimen Preparation ◽

Gold Films ◽

Boundary Area ◽

Transmission Electron ◽

Recent Developments ◽

Tilt Boundaries ◽

High Resolution Microscopy ◽

Twist Boundaries

Recent developments in specimen preparation, imaging and image analysis together permit the experimental determination of the atomic structure of certain, simple grain boundaries in metals such as gold. Single crystal, ∼125Å thick, (110) oriented gold films are vapor deposited onto ∼3000Å of epitaxial silver on (110) oriented cut and polished rock salt substrates. Bicrystal gold films are then made by first removing the silver coated substrate and placing in contact two suitably misoriented pieces of the gold film on a gold grid. Controlled heating in a hot stage first produces twist boundaries which then migrate, so reducing the grain boundary area, to give mixed boundaries and finally tilt boundaries perpendicular to the foil. These specimens are well suited to investigation by high resolution transmission electron microscopy.

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High-Resolution Image Simulation of a Tilted Crystal

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100179099 ◽

1990 ◽

Vol 48 (1) ◽

pp. 68-69

Author(s):

C. J. D. Hetherington

Keyword(s):

High Resolution ◽

Crystal Thickness ◽

Thin Specimen ◽

Atomic Structures ◽

Kikuchi Lines ◽

High Resolution Images ◽

Final Estimate ◽

Simulated Images ◽

Habit Planes

Most high resolution images are not directly interpretable but must be compared with simulations based on model atomic structures and appropriate imaging conditions. Typically, the only parameters that are adjusted, in addition to the structure models, are crystal thickness and microscope defocus. Small tilts of the crystal away from the exact zone axis have only rarely been considered. It is shown here that, in the analysis of an image of a silicon twin intersection, the crystal tilt could be accurately estimated and satisfactorily included in the simulations.The micrograph shown in figure 1 was taken as part of an HREM study of indentation-induced hexagonal silicon. In this instance, the intersection of two twins on different habit planes has driven the silicon into hexagonal stacking. However, in order to confirm this observation, and in order to investigate other defects in the region, it has been necessary to simulate the image taking into account the very apparent crystal tilt. The inability to orientate the specimen at the exact [110] zone was influenced by i) the buckling of the specimen caused by strains at twin intersections, ii) the absence of Kikuchi lines or a clearly visible Laue circle in the diffraction pattern of the thin specimen and iii) the avoidance of radiation damage (which had marked effects on images taken a few minutes later following attempts to realign the crystal.) The direction of the crystal tilt was estimated by observing which of the {111} planes remained close to edge-on to the beam and hence strongly imaged. Further refinement of the direction and magnitude of the tilt was done by comparing simulated images to experimental images in a through-focal series. The presence of three different orientations of the silicon lattice aided the unambiguous determination of the tilt. The final estimate of a 0.8° tilt in the 200Å thick specimen gives atomic columns a projected width of about 3Å.

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