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Highlights of Coronavirus Structural Studies

12 Jul

A SARS-CoV-2 neutralizing antibody with extensive Spike binding coverage and modified for optimal therapeutic outcomes (Nature Communications)

COVID-19 pandemic caused by SARS-CoV-2 constitutes a global public health crisis with enormous economic consequences. Monoclonal antibodies against SARS-CoV-2 can provide an important treatment option to fight COVID-19, especially for the most vulnerable populations. In this work, potent antibodies binding to SARS-CoV-2 Spike protein were identified from COVID-19 convalescent patients. Among them, P4A1 interacts directly with and covers majority of the Receptor Binding Motif of the Spike Receptor-Binding Domain, shown by high-resolution complex structure analysis. We further demonstrate the binding and neutralizing activities of P4A1 against wild type and mutant Spike proteins or pseudoviruses. P4A1 was subsequently engineered to reduce the potential risk for Antibody-Dependent Enhancement of infection and to extend its half-life. The engineered antibody exhibits an optimized pharmacokinetic and safety profile, and it results in complete viral clearance in a rhesus monkey model of COVID-19 following a single injection. These data suggest its potential against SARS-CoV-2 related diseases. Antibodies against SARS-CoV-2 S protein can provide a treatment strategy for COVID-19. Here, Guo et al. provide the crystal structure of a SARS-CoV2 neutralizing antibody isolated from a convalescent patient and highlight the therapeutic efficacy in a rhesus monkey model of an engineered version with optimized pharmacokinetic and safety profile.

Coronavirus Archive

Research Highlights

the best of science obtained using CIISB Core Facilities

PNAS 2021

Structure of virion of rhinovirus 14 contains resolved density corre- sponding to octanucleotides from its RNA genome. (A) Surface representa- tion of cryo-EM of reconstruction of virion of rhinovirus 14 with front half of the particle removed to show internal structure. Density corresponding to VP1 is shown in blue, VP2 in green, VP3 in red, VP4 in yellow, and RNA segments in pink. Borders of a selected icosahedral asymmetric unit are in- dicated with a dashed triangle and positions of selected twofold, threefold, and fivefold symmetry axes are represented by an oval, triangle, and pen- tagon, respectively. (Scale bar, 5 nm.) (B) Cartoon representation of icosa- hedral asymmetric unit of rhinovirus 14 viewed from the inside of the capsid. The color coding of individual virus components is the same as in A. Positions of twofold, threefold, and fivefold symmetry axes are represented by an oval, triangle, and pentagon, respectively. (C) Two RNA octanucleotides that interact with each other and with VP2 subunits. Protein and RNA coloring is the same as in A. The cryo-EM density of the RNA segments is shown as a pink semitransparent surface. RNA bases and side chains of Trp38 of VP2 are shown in stick representation, in orange, and indicated with black arrow- heads. The position of a twofold symmetry axis is indicated with an oval. (D) Detail of stacking interaction between Gua2 from RNA segment and Trp38 of VP2. The cryo-EM densities of RNA and protein are shown as semitrans- parent surfaces in pink and gray, respectively. (E) Interaction between N ter- minus of VP1 and genome. Capsid proteins are shown in cartoon representation with the same coloring as in A. Cryo-EM densities of individual proteins are shown as semitransparent surfaces colored according to the chain they belong to. The density of the RNA genome is shown in gray. The blue arrow indicates the contact between the N terminus of VP1 and the genome. The position of Thr17, the first modeled residue from the N terminus of VP1, is indicated.

Pavel Plevka Research Group

Significance

Most rhinoviruses, which are the leading cause of the common cold, utilize intercellular adhesion molecule-1 (ICAM-1) as a receptor to infect cells. To release their genomes, rhinoviruses convert to acti- vated particles that contain pores in the capsid, lack minor capsid protein VP4, and have an altered genome organization. The binding of rhinoviruses to ICAM-1 promotes virus activation; however, the molecular details of the process remain unknown. Here, we present the structures of virion of rhinovirus 14 and its complex with ICAM-1 determined to resolutions of 2.6 and 2.4 Å, respectively. The cryo- electron microscopy reconstruction of rhinovirus 14 virions contains the resolved density of octanucleotide segments from the RNA ge- nome that interact with VP2 subunits. We show that the binding of ICAM-1 to rhinovirus 14 is required to prime the virus for activation and genome release at acidic pH. Formation of the rhinovirus 14– ICAM-1 complex induces conformational changes to the rhinovirus 14 capsid, including translocation of the C termini of VP4 subunits, which become poised for release through pores that open in the capsids of activated particles. VP4 subunits with altered conforma- tion block the RNA–VP2 interactions and expose patches of posi- tively charged residues. The conformational changes to the capsid induce the redistribution of the virus genome by altering the capsid–RNA interactions. The restructuring of the rhinovirus 14 cap- sid and genome prepares the virions for conversion to activated particles. The high-resolution structure of rhinovirus 14 in complex with ICAM-1 explains how the binding of uncoating receptors en- ables enterovirus genome release.

Hrebik, D. ; Fuzik, T. ; Gondova, M. ; Smerdova, L. ; Adamopoulos, A. ; Sedo, O.; Zdrahal, Z., and Plevka, P.: ICAM-1 induced rearrangements of capsid and genome prime rhinovirus 14 for activation and uncoating, PNAS 2021 Vol. 118 No. 19 e2024251118, https://doi.org/10.1073/pnas.2024251118

 

Nature Communications 2021

Nature Index Journal

Cryo-EM structure of TEL bound to the yeast ribosome. a Transverse section of the cryo-EM map density (gray) of the large (60S) subunit of the yeast G2400A mutant ribosome with TEL (salmon) bound within the NPET. b Isolated cryo-EM density for TEL (gray mesh) with fitted molecular model for TEL. The similarly-oriented chemical structure of TEL is shown for reference. c TEL bound within the NPET with the surrounding nucleotides of the 25S rRNA (gray) and His133 residue of uL22 protein (purple). The N1 of A2400(A2058) forms a hydrogen bond interaction to the hydroxyl group of the desosamine sugar of TEL and a water molecule (W1) mediates interaction of the desosamine’s dimethylamine with the N6 of A2400(A2058), as was also observed in bacteria43. The alkyl–aryl sidechain of TEL stacks upon the base pair A884(A752)-U2978(U2609) and forms bridging interaction with water W2 (light blue) and O6 of G880(G748). d Superposition of TEL bound to the E. coli ribosome (green, PDB ID 4V7S15) with TEL (salmon) in complex with the S. cerevisiae 60S subunit (Sc60S) bearing the G2400A mutation. E. coli rRNA and ribosomal protein residues are light green, yeast rRNA and protein residues are gray.

Daniel N. Wilson and Alexander S. Mankin Research Group

Significance

Macrolide antibiotics bind in the nascent peptide exit tunnel of the bacterial ribosome and prevent polymerization of specific amino acid sequences, selectively inhibiting translation of a subset of proteins. Because preventing translation of individual proteins could be beneficial for the treatment of human diseases, we asked whether macrolides, if bound to the eukar- yotic ribosome, would retain their context- and protein-specific action. By introducing a single mutation in rRNA, we rendered yeast Saccharomyces cerevisiae cells sensitive to macrolides. Cryo-EM structural analysis showed that the macrolide telithromycin binds in the tunnel of the engineered eukaryotic ribosome. Genome-wide analysis of cellular translation and bio- chemical studies demonstrated that the drug inhibits eukaryotic translation by preferentially stalling ribosomes at distinct sequence motifs. Context-specific action markedly depends on the macrolide structure. Eliminating macrolide-arrest motifs from a protein renders its translation macrolide-tolerant. Our data illuminate the prospects of adapting macrolides for protein-selective translation inhibition in eukaryotic cells.

Svetlov, M.S.; Koller, T.O.; Meydan, S.; Shankar, V.; Klepacki, D.; Polacek, N.; Guydosh, N.. Vazquez-Laslop, N.; Wilson, D.N., and Mankin, A.S.: Context-specific action of macrolide antibiotics on the eukaryotic ribosome, Nature Comm. (2021)12:2803 https://doi.org/10.1038/s41467-021-23068-1

 

 

More publications Research Highlights archive

Reader’s Corner

literature to read, science to follow

In this section, a distinct selection of six highly stimulating research publications and reviews published during past 6 months is presented. It is our hope that links to exciting science, which deserves attention of the structural biology community, will help you to locate gems in the steadily expanding jungle of scientific literature. You are welcome to point out to any paper you found interesting by sending a link or citation to readerscorner@ciisb.org. The section is being updated regularly.


 

Reader’s Corner Archive

Quote of July

“No amount of experimentation can ever prove me right; a single experiment can prove me wrong.”

Albert Einstein

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