scholarly journals Structure of a germline-like human antibody defines a neutralizing epitope on the SARS-CoV-2 spike NTD

2021 ◽  
Author(s):  
Clara Gilda Altomare ◽  
Daniel Cole Adelsberg ◽  
Juan Manuel Carreno ◽  
Iden Avery Sapse ◽  
Fatima Amanat ◽  
...  
Keyword(s):  
Arms Race ◽  
Human Antibody ◽  
Neutralizing Epitope ◽  
Vaccine Immunogen ◽  
Direct Competition ◽  
High Resolution Structure ◽  
Immunogen Design ◽  
Insight Into ◽  
Resolution Structure

Structural characterization of infection- and vaccination-elicited antibodies in complex with antigen provides insight into the evolutionary arms race between the host and the pathogen and informs rational vaccine immunogen design. We isolated a germline-like monoclonal antibody (mAb) from plasmablasts activated upon mRNA vaccination against SARS-CoV-2 and determined its structure in complex with the spike glycoprotein by cryo-EM. We show that the mAb engages a previously uncharacterized neutralizing epitope on the spike N-terminal domain (NTD). The high-resolution structure reveals details of the intermolecular interactions and shows that the mAb inserts its HCDR3 loop into a hydrophobic NTD cavity previously shown to bind a heme metabolite, biliverdin. We demonstrate direct competition with biliverdin and that - because of the conserved nature of the epitope - the mAb maintains binding to viral variants B.1.1.7 and B.1.351. Our study illustrates the feasibility of targeting the NTD to achieve broad neutralization against SARS-CoV-2 variants.

scholarly journals Rational development of a human antibody cocktail that deploys multiple functions to confer Pan-SARS-CoVs protection

Cell Research ◽  
2020 ◽  
Vol 31 (1) ◽  
pp. 25-36 ◽  
Author(s):  
Hangping Yao ◽  
Yao Sun ◽  
Yong-Qiang Deng ◽  
Nan Wang ◽  
Yongcong Tan ◽  
...  
Keyword(s):  
Neutralizing Antibody ◽  
Human Antibody ◽  
High Potency ◽  
Rational Development ◽  
Viral Mutation ◽  
High Resolution Structure ◽  
Structural Principles ◽  
Viral Membrane Fusion ◽  
Antibody Cocktail ◽  
Resolution Structure

AbstractStructural principles underlying the composition and synergistic mechanisms of protective monoclonal antibody cocktails are poorly defined. Here, we exploited antibody cooperativity to develop a therapeutic antibody cocktail against SARS-CoV-2. On the basis of our previously identified humanized cross-neutralizing antibody H014, we systematically analyzed a fully human naive antibody library and rationally identified a potent neutralizing antibody partner, P17, which confers effective protection in animal model. Cryo-EM studies dissected the nature of the P17 epitope, which is SARS-CoV-2 specific and distinctly different from that of H014. High-resolution structure of the SARS-CoV-2 spike in complex with H014 and P17, together with functional investigations revealed that in a two-antibody cocktail, synergistic neutralization was achieved by S1 shielding and conformational locking, thereby blocking receptor attachment and viral membrane fusion, conferring high potency as well as robustness against viral mutation escape. Furthermore, cluster analysis identified a hypothetical 3rd antibody partner for further reinforcing the cocktail as pan-SARS-CoVs therapeutics.

scholarly journals Structural characterization of a potent humanized anti-CD38 antibody in phase I

2014 ◽  
Vol 70 (a1) ◽  
pp. C1813-C1813
Author(s):  
Francois Vallée ◽  
Stephanie Pouzieux ◽  
Alexey Rak ◽  
François Michoux ◽  
Marie-Cécile Wetzel ◽  
...  
Keyword(s):  
Epitope Mapping ◽  
Plasma Cells ◽  
In Vitro Assays ◽  
Strong Inhibitor ◽  
Transmembrane Glycoprotein ◽  
High Resolution Structure ◽  
Apoptotic Activity ◽  
Resolution Structure

CD38 is a type II transmembrane glycoprotein with both ADP-rybosyl cyclase and glycohydrolase activities. CD38 is highly expressed at the surface of malignant plasma cells of multiple myeloma. SAR650984 is a humanized IgG1 antibody targeting CD38 in early clinical developement that is acting through several potential mechanisms including ADCC, CDC and pro-apoptotic activity. Here we report further preclinical characterization of SAR650984 with a high resolution structure of Fab-SAR650984 in complex with CD38 allowing an epitope mapping. The crystal structure of SAR650984-Fab/huCD38 complex shows that SAR650984 neither blocks the access nor alters the configuration of the ADPRC catalytic site of CD38 although in vitro assays have demonstrated that SAR650984 behaves as a strong inhibitor of the ADPRC activity of CD38. These results suggest that SAR650984 is likely an allosteric antagonist of CD38 that alters the dynamics of enzyme upon binding.

scholarly journals High-Resolution Structure of the Histidine-Containing Phosphocarrier Protein (HPr) from Staphylococcus aureus and Characterization of Its Interaction with the Bifunctional HPr Kinase/Phosphorylase

2004 ◽  
Vol 186 (17) ◽  
pp. 5906-5918 ◽  
Author(s):  
Till Maurer ◽  
Sebastian Meier ◽  
Norman Kachel ◽  
Claudia Elisabeth Munte ◽  
Sonja Hasenbein ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
High Resolution ◽  
Core Protein ◽  
Phosphorylation Site ◽  
Hydroxyl Group ◽  
Nmr Data ◽  
High Resolution Structure ◽  
Structural Restraints ◽  
Resolution Structure

ABSTRACT A high-resolution structure of the histidine-containing phosphocarrier protein (HPr) from Staphylococcus aureus was obtained by heteronuclear multidimensional nuclear magnetic resonance (NMR) spectroscopy on the basis of 1,766 structural restraints. Twenty-three hydrogen bonds in HPr could be directly detected by polarization transfer from the amide nitrogen to the carbonyl carbon involved in the hydrogen bond. Differential line broadening was used to characterize the interaction of HPr with the HPr kinase/phosphorylase (HPrK/P) of Staphylococcus xylosus, which is responsible for phosphorylation-dephosphorylation of the hydroxyl group of the regulatory serine residue at position 46. The dissociation constant Kd was determined to be 0.10 ± 0.02 mM at 303 K from the NMR data, assuming independent binding. The data are consistent with a stoichiometry of 1 HPr molecule per HPrK/P monomer in solution. Using transversal relaxation optimized spectroscopy-heteronuclear single quantum correlation, we mapped the interaction site of the two proteins in the 330-kDa complex. As expected, it covers the region around Ser46 and the small helix b following this residue. In addition, HPrK/P also binds to the second phosphorylation site of HPr at position 15. This interaction may be essential for the recognition of the phosphorylation state of His15 and the phosphorylation-dependent regulation of the kinase/phosphorylase activity. In accordance with this observation, the recently published X-ray structure of the HPr/HPrK core protein complex from Lactobacillus casei shows interactions with the two phosphorylation sites. However, the NMR data also suggest differences for the full-length protein from S. xylosus: there are no indications for an interaction with the residues preceding the regulatory Ser46 residue (Thr41 to Lys45) in the protein of S. xylosus. In contrast, it seems to interact with the C-terminal helix of HPr in solution, an interaction which is not observed for the complex of HPr with the core of HPrK/P of L. casei in crystals.

Characterization of the Chitinolytic Machinery of Enterococcus faecalis V583 and High-Resolution Structure of Its Oxidative CBM33 Enzyme

2012 ◽  
Vol 416 (2) ◽  
pp. 239-254 ◽  
Author(s):  
Gustav Vaaje-Kolstad ◽  
Liv Anette Bøhle ◽  
Sigrid Gåseidnes ◽  
Bjørn Dalhus ◽  
Magnar Bjørås ◽  
...  
Keyword(s):  
High Resolution ◽  
Enterococcus Faecalis ◽  
High Resolution Structure ◽  
Resolution Structure

A High-Resolution Structure that Provides Insight into Coiled-Coil Thiodepsipeptide Dynamic Chemistry

2013 ◽  
Vol 52 (38) ◽  
pp. 9944-9947 ◽  
Author(s):  
Zehavit Dadon ◽  
Manickasundaram Samiappan ◽  
Anat Shahar ◽  
Raz Zarivach ◽  
Gonen Ashkenasy
Keyword(s):  
High Resolution ◽  
Coiled Coil ◽  
High Resolution Structure ◽  
Insight Into ◽  
Resolution Structure

scholarly journals High-resolution structure of AKR1a4 in the apo form and its interaction with ligands

2012 ◽  
Vol 68 (11) ◽  
pp. 1271-1274 ◽  
Author(s):  
Frédérick Faucher ◽  
Zongchao Jia
Keyword(s):  
Crystal Structure ◽  
High Resolution ◽  
Aldehyde Reductase ◽  
Founding Member ◽  
High Resolution Structure ◽  
Ascorbate Biosynthesis ◽  
Resolution Structure

Aldo-keto reductase 1a4 (AKR1a4; EC 1.1.1.2) is the mouse orthologue of human aldehyde reductase (AKR1a1), the founding member of the AKR family. As an NADPH-dependent enzyme, AKR1a4 catalyses the conversion of D-glucuronate to L-gulonate. AKR1a4 is involved in ascorbate biosynthesis in mice, but has also recently been found to interact with SMAR1, providing a novel mechanism of ROS regulation by ATM. Here, the crystal structure of AKR1a4 in its apo form at 1.64 Å resolution as well as the characterization of the binding of AKR1a4 to NADPH and P44, a peptide derived from SMAR1, is presented.

scholarly journals Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jerzy Osipiuk ◽  
Saara-Anne Azizi ◽  
Steve Dvorkin ◽  
Michael Endres ◽  
Robert Jedrzejczak ◽  
...  
Keyword(s):  
Host Responses ◽  
Peptidase Activity ◽  
Clinical Value ◽  
Structure Based Drug Design ◽  
Replication Studies ◽  
Covalent Inhibitors ◽  
High Resolution Structure ◽  
Insight Into ◽  
Resolution Structure

AbstractThe pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) continues to expand. Papain-like protease (PLpro) is one of two SARS-CoV-2 proteases potentially targetable with antivirals. PLpro is an attractive target because it plays an essential role in cleavage and maturation of viral polyproteins, assembly of the replicase-transcriptase complex, and disruption of host responses. We report a substantive body of structural, biochemical, and virus replication studies that identify several inhibitors of the SARS-CoV-2 enzyme. We determined the high resolution structure of wild-type PLpro, the active site C111S mutant, and their complexes with inhibitors. This collection of structures details inhibitors recognition and interactions providing fundamental molecular and mechanistic insight into PLpro. All compounds inhibit the peptidase activity of PLpro in vitro, some block SARS-CoV-2 replication in cell culture assays. These findings will accelerate structure-based drug design efforts targeting PLpro to identify high-affinity inhibitors of clinical value.

scholarly journals High-Resolution Structure of Cas13b and Biochemical Characterization of RNA Targeting and Cleavage

Cell Reports ◽  
2019 ◽  
Vol 26 (13) ◽  
pp. 3741-3751.e5 ◽  
Author(s):  
Ian M. Slaymaker ◽  
Pablo Mesa ◽  
Max J. Kellner ◽  
Soumya Kannan ◽  
Edward Brignole ◽  
...  
Keyword(s):  
High Resolution ◽  
Biochemical Characterization ◽  
Rna Targeting ◽  
High Resolution Structure ◽  
Resolution Structure

scholarly journals Dysregulation of Microtubule Nucleating Proteins in Cancer Cells

Cancers ◽  
2021 ◽  
Vol 13 (22) ◽  
pp. 5638
Author(s):  
Pavel Dráber ◽  
Eduarda Dráberová
Keyword(s):  
Cancer Cells ◽  
Cell Behavior ◽  
Microtubule Nucleation ◽  
Microtubule Targeting Agents ◽  
High Resolution Structure ◽  
Ring Complex ◽  
New Compounds ◽  
Centrosomal Proteins ◽  
Insight Into ◽  
Resolution Structure

In cells, microtubules typically nucleate from microtubule organizing centers, such as centrosomes. γ-Tubulin, which forms multiprotein complexes, is essential for nucleation. The γ-tubulin ring complex (γ-TuRC) is an efficient microtubule nucleator that requires additional centrosomal proteins for its activation and targeting. Evidence suggests that there is a dysfunction of centrosomal microtubule nucleation in cancer cells. Despite decades of molecular analysis of γ-TuRC and its interacting factors, the mechanisms of microtubule nucleation in normal and cancer cells remains obscure. Here, we review recent work on the high-resolution structure of γ-TuRC, which brings new insight into the mechanism of microtubule nucleation. We discuss the effects of γ-TuRC protein dysregulation on cancer cell behavior and new compounds targeting γ-tubulin. Drugs inhibiting γ-TuRC functions could represent an alternative to microtubule targeting agents in cancer chemotherapy.

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