scholarly journals Structures of the Omicron spike trimer with ACE2 and an anti-Omicron antibody: mechanisms for the high infectivity, immune evasion and antibody drug discovery

2021 ◽  
Author(s):  
Wanchao Yin ◽  
Youwei Xu ◽  
Peiyu Xu ◽  
Xiaodan Cao ◽  
Canrong Wu ◽  
...  
Keyword(s):  
Immune Evasion ◽  
Phase 1 ◽  
Spike Protein ◽  
Structural Basis ◽  
Phase 1 Clinical Trial ◽  
Closed Conformation ◽  
Open Conformation ◽  
Potent Inhibition ◽  
Antibody Drug ◽  
High Infectivity

The Omicron variant of SARS-CoV-2 has rapidly become the dominant infective strain and the focus efforts against the ongoing COVID-19 pandemic. Here we report an extensive set of structures of the Omicron spike trimer by its own or in complex with ACE2 and an anti-Omicron antibody. These structures reveal that most Omicron mutations are located on the surface of the spike protein, which confer stronger ACE2 binding by nearly 10 folds but become inactive epitopes resistant to many therapeutic antibodies. Importantly, both RBD and the closed conformation of the Omicron spike trimer are thermodynamically unstable, with the melting temperature of the Omicron RBD decreased by as much as 7 degree, making the spiker trimer prone to random open conformations. An unusual RBD-RBD interaction in the ACE2-spike complex unique to Omicron is observed to support the open conformation and ACE2 binding, serving the basis for the higher infectivity of Omicron. A broad-spectrum therapeutic antibody JMB2002, which has completed Phase 1 clinical trial, is found to interact with the same two RBDs to inhibit ACE2 binding, in a mode that is distinguished from all previous antibodies, thus providing the structural basis for the potent inhibition of Omicron by this antibody. Together with biochemical data, our structures provide crucial insights into higher infectivity, antibody evasion and inhibition of Omicron.

scholarly journals Structural and functional analysis of the human spliceosomal DEAD-box helicase Prp28

2014 ◽  
Vol 70 (6) ◽  
pp. 1622-1630 ◽  
Author(s):  
Sina Möhlmann ◽  
Rebecca Mathew ◽  
Piotr Neumann ◽  
Andreas Schmitt ◽  
Reinhard Lührmann ◽  
...  
Keyword(s):  
Binding Activity ◽  
Mrna Splicing ◽  
Structural Basis ◽  
Atp Binding ◽  
Helicase Domain ◽  
Crucial Step ◽  
Closed Conformation ◽  
Dead Box ◽  
Open Conformation ◽  
U1 Snrnp

The DEAD-box protein Prp28 is essential for pre-mRNA splicing as it plays a key role in the formation of an active spliceosome. Prp28 participates in the release of the U1 snRNP from the 5′-splice site during association of the U5·U4/U6 tri-snRNP, which is a crucial step in the transition from a pre-catalytic spliceosome to an activated spliceosome. Here, it is demonstrated that the purified helicase domain of human Prp28 (hPrp28ΔN) binds ADP, whereas binding of ATP and ATPase activity could not be detected. ATP binding could not be observed for purified full-length hPrp28 either, but within an assembled spliceosomal complex hPrp28 gains ATP-binding activity. In order to understand the structural basis for the ATP-binding deficiency of isolated hPrp28, the crystal structure of hPrp28ΔN was determined at 2.0 Å resolution. In the crystal the helicase domain adopts a wide-open conformation, as the two RecA-like domains are extraordinarily displaced from the productive ATPase conformation. Binding of ATP is hindered by a closed conformation of the P-loop, which occupies the space required for the γ-phosphate of ATP.

scholarly journals Structural basis for adenylation and thioester bond formation in the ubiquitin E1

2019 ◽  
Vol 116 (31) ◽  
pp. 15475-15484 ◽  
Author(s):  
Zachary S. Hann ◽  
Cheng Ji ◽  
Shaun K. Olsen ◽  
Xuequan Lu ◽  
Michaelyn C. Lux ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Biochemical Analysis ◽  
Bond Formation ◽  
Structural Basis ◽  
Closed Conformation ◽  
Open Conformation ◽  
Thioester Bond ◽  
Catalytic Cysteine ◽  
Conjugating Enzymes ◽  
Insight Into

The ubiquitin (Ub) and Ub-like (Ubl) protein-conjugation cascade is initiated by E1 enzymes that catalyze Ub/Ubl activation through C-terminal adenylation, thioester bond formation with an E1 catalytic cysteine, and thioester bond transfer to Ub/Ubl E2 conjugating enzymes. Each of these reactions is accompanied by conformational changes of the E1 domain that contains the catalytic cysteine (Cys domain). Open conformations of the Cys domain are associated with adenylation and thioester transfer to E2s, while a closed conformation is associated with pyrophosphate release and thioester bond formation. Several structures are available for Ub E1s, but none has been reported in the open state before pyrophosphate release or in the closed state. Here, we describe the structures ofSchizosaccharomyces pombeUb E1 in these two states, captured using semisynthetic Ub probes. In the first, with a Ub-adenylate mimetic (Ub-AMSN) bound, the E1 is in an open conformation before release of pyrophosphate. In the second, with a Ub-vinylsulfonamide (Ub-AVSN) bound covalently to the catalytic cysteine, the E1 is in a closed conformation required for thioester bond formation. These structures provide further insight into Ub E1 adenylation and thioester bond formation. Conformational changes that accompany Cys-domain rotation are conserved for SUMO and Ub E1s, but changes in Ub E1 involve additional surfaces as mutational and biochemical analysis of residues within these surfaces alter Ub E1 activities.

scholarly journals Molecular switches regulating the potency and immune evasiveness of SARS-CoV-2 spike protein

2021 ◽  
Author(s):  
Yushun Wan ◽  
Linfen Huang ◽  
Xiujuan Zhang ◽  
Jian Shang ◽  
Stanley Perlman ◽  
...  
Keyword(s):  
Viral Entry ◽  
Neutralizing Antibodies ◽  
Molecular Switches ◽  
Spike Protein ◽  
Structural Determinants ◽  
Future Evolution ◽  
Viral Immune Evasion ◽  
Closed Conformation ◽  
Open Conformation ◽  
Global Pandemic

Abstract What enabled SARS-CoV-2, but not other coronaviruses, to cause a global pandemic? Here we investigated key structural determinants of the pandemic. Using SARS-CoV-1 and bat RaTG13-CoV as comparisons, we identified two molecular switches that regulate the conformations of SARS-CoV-2 spike protein: (i) a furin motif loop turns SARS-CoV-2 spike from a closed conformation to a mixture of open and closed conformations, and (ii) a K417V mutation turns SARS-CoV-2 spike from mixed conformations to an open conformation. We showed that the open conformation favors viral potency by exposing the RBD for receptor binding and viral entry, while the closed conformation supports viral immune evasion by hiding the RBD from neutralizing antibodies. Hence SARS-CoV-2 spike has evolved to reach a balance between potency and immune evasiveness, which contributes to the pandemic spread of SARS-CoV-2.The dynamics between viral potency and invasiveness is likely to further evolve, providing insights into future evolution of SARS-CoV-2.

scholarly journals Molecular switches regulating the potency and immune evasiveness of SARS-CoV-2 spike protein

2021 ◽  
Author(s):  
Yushun Wan ◽  
Linfen Huang ◽  
Xiujuan Zhang ◽  
Jian Shang ◽  
Stanley Perlman ◽  
...  
Keyword(s):  
Viral Entry ◽  
Neutralizing Antibodies ◽  
Molecular Switches ◽  
Spike Protein ◽  
Structural Determinants ◽  
Future Evolution ◽  
Viral Immune Evasion ◽  
Closed Conformation ◽  
Open Conformation ◽  
Global Pandemic

Abstract What enabled SARS-CoV-2, but not other coronaviruses, to cause a global pandemic? Here we investigated key structural determinants of the pandemic. Using SARS-CoV-1 and bat RaTG13-CoV as comparisons, we identified two molecular switches that regulate the conformations of SARS-CoV-2 spike protein: (i) a furin motif loop turns SARS-CoV-2 spike from a closed conformation to a mixture of open and closed conformations, and (ii) a K417V mutation turns SARS-CoV-2 spike from mixed conformations to an open conformation. We showed that the open conformation favors viral potency by exposing the RBD for receptor binding and viral entry, while the closed conformation supports viral immune evasion by hiding the RBD from neutralizing antibodies. Hence SARS-CoV-2 spike has evolved to reach a balance between potency and immune evasiveness, which contributes to the pandemic spread of SARS-CoV-2.The dynamics between viral potency and invasiveness is likely to further evolve, providing insights into future evolution of SARS-CoV-2.

scholarly journals Structural analysis of the SRP Alu domain from Plasmodium falciparum reveals a non-canonical open conformation

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Komal Soni ◽  
Georg Kempf ◽  
Karen Manalastas-Cantos ◽  
Astrid Hendricks ◽  
Dirk Flemming ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Binding Sites ◽  
Signal Recognition Particle ◽  
Signal Recognition ◽  
Closed Conformation ◽  
Open Conformation ◽  
Structural Database ◽  
Alu Rna ◽  
Species Specific ◽  
Protozoan Species

AbstractThe eukaryotic signal recognition particle (SRP) contains an Alu domain, which docks into the factor binding site of translating ribosomes and confers translation retardation. The canonical Alu domain consists of the SRP9/14 protein heterodimer and a tRNA-like folded Alu RNA that adopts a strictly ‘closed’ conformation involving a loop-loop pseudoknot. Here, we study the structure of the Alu domain from Plasmodium falciparum (PfAlu), a divergent apicomplexan protozoan that causes human malaria. Using NMR, SAXS and cryo-EM analyses, we show that, in contrast to its prokaryotic and eukaryotic counterparts, the PfAlu domain adopts an ‘open’ Y-shaped conformation. We show that cytoplasmic P. falciparum ribosomes are non-discriminative and recognize both the open PfAlu and closed human Alu domains with nanomolar affinity. In contrast, human ribosomes do not provide high affinity binding sites for either of the Alu domains. Our analyses extend the structural database of Alu domains to the protozoan species and reveal species-specific differences in the recognition of SRP Alu domains by ribosomes.

scholarly journals Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil

Science ◽  
2021 ◽  
pp. eabh2644 ◽  
Author(s):  
Nuno R. Faria ◽  
Thomas A. Mellan ◽  
Charles Whittaker ◽  
Ingra M. Claro ◽  
Darlan da S. Candido ◽  
...  
Keyword(s):  
Molecular Evolution ◽  
Genome Sequencing ◽  
Immune Evasion ◽  
Molecular Clock ◽  
Spike Protein ◽  
Dynamical Model ◽  
Mortality Data ◽  
Clock Analysis ◽  
Protection Against Infection ◽  
Molecular Clock Analysis

Cases of SARS-CoV-2 infection in Manaus, Brazil, resurged in late 2020, despite previously high levels of infection. Genome sequencing of viruses sampled in Manaus between November 2020 and January 2021 revealed the emergence and circulation of a novel SARS-CoV-2 variant of concern. Lineage P.1, acquired 17 mutations, including a trio in the spike protein (K417T, E484K and N501Y) associated with increased binding to the human ACE2 receptor. Molecular clock analysis shows that P.1 emergence occurred around mid-November 2020 and was preceded by a period of faster molecular evolution. Using a two-category dynamical model that integrates genomic and mortality data, we estimate that P.1 may be 1.7–2.4-fold more transmissible, and that previous (non-P.1) infection provides 54–79% of the protection against infection with P.1 that it provides against non-P.1 lineages. Enhanced global genomic surveillance of variants of concern, which may exhibit increased transmissibility and/or immune evasion, is critical to accelerate pandemic responsiveness.

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