Abstract:Single-spanning SARS-CoV-2 envelope (E) protein topology is a major determinant of protein quaternary structure and function.
Charged residues distribution in E protein sequences from highly pathogenic human coronaviruses (
i.e.
, SARS-CoV, MERS-CoV and SARS-CoV-2) stabilize Nt out -Ct in membrane topology.
E protein sequence could have evolved to ensure a more robust membrane topology from MERS-CoV to SARS-CoV and SARS-CoV-2.
“…Notably, envelope proteins have recently been shown to slow the secretory pathway (Boson et al, 2021;Denolly et al, 2017). However, since the exact topology of the E protein remains unclear, we cannot presently deduce the precise mechanism by which this event occurs, although interesting speculations have been proposed (Duart et al, 2021;reviewed in Schoeman & Fielding, 2019).…”
SARS-CoV-2 is the virus responsible for the COVID-19 pandemic which continues to wreak havoc across the world, over a year and a half after its effects were first reported in the general media. Current fundamental research efforts largely focus on the SARS-CoV-2 Spike protein. Since successful antiviral therapies are likely to target multiple viral components, there is considerable interest in understanding the biophysical role of its other proteins, in particular structural membrane proteins. Here, we have focused our efforts on the characterization of the full-length E protein from SARS-CoV-2, combining experimental and computational approaches. Recombinant expression of the full-length E protein from SARS-CoV-2 reveals that this membrane protein is capable of independent multimerization, possibly as a tetrameric or smaller species. Fluorescence microscopy shows that the protein localizes intracellularly, and coarse-grained MD simulations indicate it causes bending of the surrounding lipid bilayer, corroborating a potential role for the E protein in viral budding. Although we did not find robust electrophysiological evidence of ion-channel activity, cells transfected with the E protein exhibited reduced intracellular Ca2+, which may further promote viral replication. However, our atomistic MD simulations revealed that previous NMR structures are relatively unstable, and result in models incapable of ion conduction. Our study highlights the importance of using high-resolution structural data obtained from a full-length protein to gain detailed molecular insights, and eventually permitting virtual drug screening.
“…Notably, envelope proteins have recently been shown to slow the secretory pathway (Boson et al, 2021;Denolly et al, 2017). However, since the exact topology of the E protein remains unclear, we cannot presently deduce the precise mechanism by which this event occurs, although interesting speculations have been proposed (Duart et al, 2021;reviewed in Schoeman & Fielding, 2019).…”
SARS-CoV-2 is the virus responsible for the COVID-19 pandemic which continues to wreak havoc across the world, over a year and a half after its effects were first reported in the general media. Current fundamental research efforts largely focus on the SARS-CoV-2 Spike protein. Since successful antiviral therapies are likely to target multiple viral components, there is considerable interest in understanding the biophysical role of its other proteins, in particular structural membrane proteins. Here, we have focused our efforts on the characterization of the full-length E protein from SARS-CoV-2, combining experimental and computational approaches. Recombinant expression of the full-length E protein from SARS-CoV-2 reveals that this membrane protein is capable of independent multimerization, possibly as a tetrameric or smaller species. Fluorescence microscopy shows that the protein localizes intracellularly, and coarse-grained MD simulations indicate it causes bending of the surrounding lipid bilayer, corroborating a potential role for the E protein in viral budding. Although we did not find robust electrophysiological evidence of ion-channel activity, cells transfected with the E protein exhibited reduced intracellular Ca2+, which may further promote viral replication. However, our atomistic MD simulations revealed that previous NMR structures are relatively unstable, and result in models incapable of ion conduction. Our study highlights the importance of using high-resolution structural data obtained from a full-length protein to gain detailed molecular insights, and eventually permitting virtual drug screening.
“…Some function as RNA-dependent RNA polymerases, in addition to binding ATP and zinc ions [ 19 , 20 ]. The E and M proteins may be involved in RNA packaging and virus assembly and release; the E protein has evolved to include a robust membrane topology, and it forms either a cation channel regulated by pH or an ion channel potentially inhibited by gliclazide and memantine [ 19 , 21 – 23 ]. The N protein, which is located inside the virion, is responsible for RNA packaging and virus replication.…”
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) initiates the infection process by binding to the viral cellular receptor angiotensin-converting enzyme 2 through the receptor-binding domain (RBD) in the S1 subunit of the viral spike (S) protein. This event is followed by virus–cell membrane fusion mediated by the S2 subunit, which allows virus entry into the host cell. Therefore, the SARS-CoV-2 S protein is a key therapeutic target, and prevention and treatment of coronavirus disease 2019 (COVID-19) have focused on the development of neutralizing monoclonal antibodies (nAbs) that target this protein. In this review, we summarize the nAbs targeting SARS-CoV-2 proteins that have been developed to date, with a focus on the N-terminal domain and RBD of the S protein. We also describe the roles that binding affinity, neutralizing activity, and protection provided by these nAbs play in the prevention and treatment of COVID-19 and discuss the potential to improve nAb efficiency against multiple SARS-CoV-2 variants. This review provides important information for the development of effective nAbs with broad-spectrum activity against current and future SARS-CoV-2 strains.
“…Similarly, Benvenuto et al showed seven transmembrane regions in NSP6 of coronaviruses by using TMHMM server and investigated the effect of mutation in NSPs and orf10 in their adjacent region [ 7 ]. Recently, SARS-CoV-2 E protein topology has been predicted and experimentally validated with the help of these servers [ 28 , 29 ]. Fig.…”
The NSP6 protein of SARS-CoV-2 is a transmembrane protein, with some regions lying outside the membrane. Besides a brief role of NSP6 in autophagosome formation, this is not studied significantly. Also, there is no structural information available to date. Based on the prediction by TMHMM server for transmembrane prediction, it is found that the N-terminal residues (Giri et al., 2020; Naqvi et al., 2020; Bojkova et al., 2020; Gordon et al., 2020; V’kovski et al., 2021; von Brunn et al., 2007; Benvenuto et al., 2020; Cottam et al., 2011; Oostra et al., 2008; Angelini et al., 2013; Schweizer et al., 2014) [1-11], middle region residues (91–112), and C-terminal residues (231–290) lies outside the membrane. Molecular Dynamics (MD) simulations showed that NSP6 consists of helical structures. In contrast, the membrane outside lying region (91–112) showed partial helicity, which was further used as a model and obtained disordered type conformation during 1.5 microseconds. Additionally, a 200ns simulation study of residues 231–290 have shown significant conformational changes. As compared to helical and beta-sheet conformations in its structure model, the 200ns simulation resulted in the loss of beta-sheet structures while helical regions remained intact. Further, we have experimentally characterized the residue 91–112 by using reductionist approaches. CD spectroscopy suggests that the NSP6 (91–112) is disordered-like region in isolation, which gains helical conformation in different biological mimic environmental conditions. These studies can be helpful to study NSP6 (91–112) interactions with host proteins, where different protein conformations might play a significant role. The present study adds up more information about the NSP6 protein aspect, which could be exploited for its host protein interaction and pathogenesis.
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