9 Sep 2022

Intermediates in SARS-CoV-2 spike-mediated cell entry (Science Advances)

SARS-CoV-2 cell entry is completed after viral spike (S) protein-mediated membrane fusion between viral and host cell membranes. Stable prefusion and postfusion S structures have been resolved by cryo-electron microscopy and cryo-electron tomography, but the refolding intermediates on the fusion pathway are transient and have not been examined. We used an antiviral lipopeptide entry inhibitor to arrest S protein refolding and thereby capture intermediates as S proteins interact with hACE2 and fusion-activating proteases on cell-derived target membranes. Cryo-electron tomography imaged both extended and partially folded intermediate states of S2, as well as a novel late-stage conformation on the pathway to membrane fusion. The intermediates now identified in this dynamic S protein-directed fusion provide mechanistic insights that may guide the design of CoV entry inhibitors.

9 Sep 2022

A public antibody class recognizes an S2 epitope exposed on open conformations of SARS-CoV-2 spike (Nature Communications)

Delineating the origins and properties of antibodies elicited by SARS-CoV-2 infection and vaccination is critical for understanding their benefits and potential shortcomings. Therefore, we investigate the SARS-CoV-2 spike (S)-reactive B cell repertoire in unexposed individuals by flow cytometry and single-cell sequencing. We show that similar to 82% of SARS-CoV-2 S-reactive B cells harbor a naive phenotype, which represents an unusually high fraction of total human naive B cells (similar to 0.1%). Approximately 10% of these naive S-reactive B cells share an IGHV1-69/IGKV3-11 B cell receptor pairing, an enrichment of 18-fold compared to the complete naive repertoire. Following SARS-CoV-2 infection, we report an average 37-fold enrichment of IGHV1-69/IGKV3-11 B cell receptor pairing in the S-reactive memory B cells compared to the unselected memory repertoire. This class of B cells targets a previously undefined non-neutralizing epitope on the S2 subunit that becomes exposed on S proteins used in approved vaccines when they transition away from the native pre-fusion state because of instability. These findings can help guide the improvement of SARS-CoV-2 vaccines.

To fully understand the potential shortcomings of SARS-CoV-2 vaccination, it is necessary to delineate the properties of the antibodies elicited, during immunization, and also infection. Through investigation of the SARS-CoV-2 spike-reactive B cell repertoire, authors identify following infection, a subset of B cells enriched and almost exclusively target a non-neutralizing S2 epitope present in aberrant forms.

9 Sep 2022

Structural insights of a highly potent pan-neutralizing SARS-CoV-2 human monoclonal antibody (PNAS)

As the coronavirus disease 2019 (COVID-19) pandemic continues, there is a strong need for highly potent monoclonal antibodies (mAbs) that are resistant against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VoCs). Here, we evaluate the potency of the previously described mAb J08 against these variants using cell-based assays and delve into the molecular details of the binding interaction using cry-oelectron microscopy (cryo-EM) and X-ray crystallography. We show that mAb J08 has low nanomolar affinity against most VoCs and binds high on the receptor binding domain (RBD) ridge, away from many VoC mutations. These findings further validate the phase II/III human clinical trial underway using mAb J08 as a monoclonal therapy.

10 Oct 2023

Structure of LARP7 Protein p65–telomerase RNA Complex in Telomerase Revealed by Cryo-EM and NMR (Journal of Molecular Biology)

La-related protein 7 (LARP7) are a family of RNA chaperones that protect the 3′-end of RNA and are components of specific ribonucleoprotein complexes (RNP). In Tetrahymena thermophila telomerase, LARP7 protein p65 together with telomerase reverse transcriptase (TERT) and telomerase RNA (TER) form the core RNP. p65 has four known domains—N-terminal domain (NTD), La motif (LaM), RNA recognition motif 1 (RRM1), and C-terminal xRRM2. To date, only the xRRM2 and LaM and their interactions with TER have been structurally characterized. Conformational dynamics leading to low resolution in cryo-EM density maps have limited our understanding of how full-length p65 specifically recognizes and remodels TER for telomerase assembly. Here, we combined focused classification of Tetrahymena telomerase cryo-EM maps with NMR spectroscopy to determine the structure of p65–TER. Three previously unknown helices are identified, one in the otherwise intrinsically disordered NTD that binds the La module, one that extends RRM1, and another preceding xRRM2, that stabilize p65–TER interactions. The extended La module (αN, LaM and RRM1) interacts with the four 3′ terminal U nucleotides, while LaM and αN additionally interact with TER pseudoknot, and LaM with stem 1 and 5′ end. Our results reveal the extensive p65–TER interactions that promote TER 3′-end protection, TER folding, and core RNP assembly and stabilization. The structure of full-length p65 with TER also sheds light on the biological roles of genuine La and LARP7 proteins as RNA chaperones and core RNP components.

10 Oct 2023

Recent Advances and Best Practices for Cryo-EM Analysis for Protein Structure Determination (Journal of Visualized Experiments)

Since the emergence of direct electron detectors and the improvement of software and hardware, cryo-electron microscopy (cryo-EM) has become a technique that routinely allows researchers to determine the structure of macromolecules to near-atomic detail. This acceleration has been catalyzed by an extremely fast-paced series of new developments, from sample preparation to data collection and processing. To allow for a wide democratization of this technique to non-experts, more efficient and accessible pipelines have been created. Strikingly, less than 10 years after the “resolution revolution”, cryo-EM has become an essential technique for protein characterization, both in academia and the industry.

10 Oct 2023

Radiation damage to biological macromolecules (Current Opinion in Structural Biology)

In this review, we describe recent research developments into radiation damage effects in macromolecular X-ray crystallography observed at synchrotrons and X-ray free electron lasers. Radiation damage in small molecule X-ray crystallography, small angle X-ray scattering experiments, microelectron diffraction, and single particle cryo-electron microscopy is briefly covered.

10 Oct 2023

cGLRs are a diverse family of pattern recognition receptors in innate immunity (Cell)

Cyclic GMP-AMP synthase (cGAS) is an enzyme in human cells that controls an immune response to cytosolic DNA. Upon binding DNA, cGAS synthesizes a nucleotide signal 2′3′-cGAMP that activates STING-dependent downstream immunity. Here, we discover that cGAS-like receptors (cGLRs) constitute a major family of pattern recognition receptors in innate immunity. Building on recent analysis in Drosophila, we identify >3,000 cGLRs present in nearly all metazoan phyla. A forward biochemical screening of 150 animal cGLRs reveals a conserved mechanism of signaling including response to dsDNA and dsRNA ligands and synthesis of isomers of the nucleotide signals cGAMP, c-UMP-AMP, and c-di-AMP. Combining structural biology and in vivo analysis in coral and oyster animals, we explain how the synthesis of distinct nucleotide signals enables cells to control discrete cGLR-STING signaling pathways. Our results reveal cGLRs as a widespread family of pattern recognition receptors and establish molecular rules that govern nucleotide signaling in animal immunity.

10 Oct 2023

Structural basis of γ chain family receptor sharing at the membrane level (Science)

Common γ chain (γc) cytokine receptors, including interleukin-2 (IL-2), IL-4, IL-7, IL-9, IL-15, and IL-21 receptors, are activated upon engagement with a common γc receptor (CD132) by concomitant binding of their ectodomains to an interleukin. In this work, we find that direct interactions between the transmembrane domains (TMDs) of both the γc and the interleukin receptors (ILRs) are also required for receptor activation. Moreover, the same γc TMD can specifically recognize multiple ILR TMDs of diverse sequences within the family. Heterodimer structures of γc TMD bound to IL-7 and IL-9 receptor TMDs—determined in a lipid bilayer–like environment by nuclear magnetic resonance spectroscopy—reveal a conserved knob-into-hole mechanism of recognition that mediates receptor sharing within the membrane. Thus, signaling in the γc receptor family requires specific heterotypic interactions of the TMDs.

10 Oct 2023

After AlphaFold: protein-folding contest seeks next big breakthrough (Nature)

Two years after DeepMind’s revolutionary AI swept a competition for predicting protein structures, researchers are building on AlphaFold’s success. “In some sense, the problem is solved,” computational biologist John Moult declared in late 2020. The London-based company DeepMind had just swept a biennial contest co-founded by Moult that tests teams’ abilities to predict protein structures — one of biology’s grandest challenges — with its revolutionary artificial-intelligence (AI) tool AlphaFold. Two years later, Moult’s competition, the Critical Assessment of Structure Prediction (CASP), is still walking in AlphaFold’s long shadow. Results from this year’s edition (CASP15) — which were unveiled over the weekend at a conference in Antalya, Turkey — show that the most successful approaches to predicting protein structures from their amino-acid sequences incorporated AlphaFold, which relies on an AI approach called deep learning. “Everyone is using AlphaFold,” says Yang Zhang, a computational biologist at the University of Michigan in Ann Arbor. Yet AlphaFold’s progress has opened the floodgates for new challenges in protein-structure prediction — some included in this year’s CASP — that might require new approaches and more time to fully tackle. “The low-hanging fruit has been picked,” says Mohammed AlQuraishi, a computational biologist at Columbia University in New York City. “Some of the next problems are going to be harder.”

29 Aug 2023

Cryo-EM structure of coagulation factor V short (Blood)

Coagulation factor V (fV) is the precursor of activated fV (fVa), an essential component of the prothrombinase complex required for the rapid activation of prothrombin in the penultimate step of the coagulation cascade. In addition, fV regulates the tissue factor pathway inhibitor α (TFPIα) and protein C pathways that inhibit the coagulation response. A recent cryogenic electron microscopy (cryo-EM) structure of fV has revealed the architecture of its A1-A2-B-A3-C1-C2 assembly but left the mechanism that keeps fV in its inactive state unresolved because of an intrinsic disorder in the B domain. A splice variant of fV, fV short, carries a large deletion of the B domain that produces constitutive fVa-like activity and unmasks epitopes for the binding of TFPIα. The cryo-EM structure of fV short was solved at 3.2 Å resolution and revealed the arrangement of the entire A1-A2-B-A3-C1-C2 assembly. The shorter B domain stretches across the entire width of the protein, making contacts with the A1, A2, and A3 domains but suspended over the C1 and C2 domains. In the portion distal to the splice site, several hydrophobic clusters and acidic residues provide a potential binding site for the basic C-terminal end of TFPIα. In fV, these epitopes may bind intramolecularly to the basic region of the B domain. The cryo-EM structure reported in this study advances our understanding of the mechanism that keeps fV in its inactive state, provides new targets for mutagenesis and facilitates future structural analysis of fV short in complex with TFPIα, protein S, and fXa.

29 Aug 2023

Principles of human pre-60S biogenesis (Science)

Human ribosome biogenesis is a highly regulated process involving a vast ensemble of assembly factors that orchestrate the formation of both ribosomal subunits. The mechanisms underlying the early assembly of the human large ribosomal subunit (pre-60S) remain elusive. To provide insights into human ribosome assembly, Vanden Broeck and Klinge used a combination of genome editing, cryo–electron microscopy, and functional studies to reveal the structures of human pre-60S particles as they matured in the nucleolus and nucleus. This collection of structures highlights how assembly factors ensure the unidirectional maturation of human large ribosomal subunit precursors. The study set out to elucidate the early stages of human pre-60S assembly at a mechanistic level. To this end, the authors have combined human genome editing and biochemistry to permeabilize human nucleoli and nuclei to isolate intact endogenous pre-60Sassembly intermediates for subsequent structural characterization by cryo–electron microscopy (cryo-EM). To functionally study rRNA processing, they developed an in vivo recombinant ribosome assembly assay using an engineered human rDNA locus to investigate whether rRNA elements within ITS2 and the 28S rRNA are required for large ribosomal subunit biogenesis.