Relating structure and function of viral membrane-spanning miniproteins

Opella, Stanley J.

doi:10.1016/j.coviro.2015.05.006

Cited by 20 publications

(18 citation statements)

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“…SARS-CoV-2 E protein is a hydrophobic 75-residue protein with an amino acid sequence nearly identical to that of SARS-CoV E protein ( S1 Fig ) [ 12 ]. Since E protein is a viral membrane-spanning miniprotein [ 16 ], a recurring question is whether it is a viroporin. Although ion-channel activity has been detected in a variety of preparations it lacks sequence homology with any of the well-established viroporins, and there is a notable absence of charged sidechains on the interior of a pore formed by pentamers of the protein in membrane environments [ 9 , 10 , 17 , 18 ].…”

Section: Introductionmentioning

confidence: 99%

Interactions of SARS-CoV-2 envelope protein with amilorides correlate with antiviral activity

et al. 2021

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SARS-CoV-2 is the novel coronavirus that is the causative agent of COVID-19, a sometimes-lethal respiratory infection responsible for a world-wide pandemic. The envelope (E) protein, one of four structural proteins encoded in the viral genome, is a 75-residue integral membrane protein whose transmembrane domain exhibits ion channel activity and whose cytoplasmic domain participates in protein-protein interactions. These activities contribute to several aspects of the viral replication-cycle, including virion assembly, budding, release, and pathogenesis. Here, we describe the structure and dynamics of full-length SARS-CoV-2 E protein in hexadecylphosphocholine micelles by NMR spectroscopy. We also characterized its interactions with four putative ion channel inhibitors. The chemical shift index and dipolar wave plots establish that E protein consists of a long transmembrane helix (residues 8–43) and a short cytoplasmic helix (residues 53–60) connected by a complex linker that exhibits some internal mobility. The conformations of the N-terminal transmembrane domain and the C-terminal cytoplasmic domain are unaffected by truncation from the intact protein. The chemical shift perturbations of E protein spectra induced by the addition of the inhibitors demonstrate that the N-terminal region (residues 6–18) is the principal binding site. The binding affinity of the inhibitors to E protein in micelles correlates with their antiviral potency in Vero E6 cells: HMA ≈ EIPA > DMA >> Amiloride, suggesting that bulky hydrophobic groups in the 5’ position of the amiloride pyrazine ring play essential roles in binding to E protein and in antiviral activity. An N15A mutation increased the production of virus-like particles, induced significant chemical shift changes from residues in the inhibitor binding site, and abolished HMA binding, suggesting that Asn15 plays a key role in maintaining the protein conformation near the binding site. These studies provide the foundation for complete structure determination of E protein and for structure-based drug discovery targeting this protein.

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Section: Introductionmentioning

confidence: 99%

Interactions of SARS-CoV-2 envelope protein with amilorides correlate with antiviral activity

et al. 2021

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“…This reduced size might reflect the need to take optimal advantage of the limited sequence information encoded in compact viral genomes, as already observed for other viral proteins (for review see ref. 31 ). On the other hand, it has been previously suggested that viral PDFs might exhibit specific distinct substrate specificity compared to bacterial PDFs 16 .…”

Section: Discussionmentioning

confidence: 99%

The C-terminal residue of phage Vp16 PDF, the smallest peptide deformylase, acts as an offset element locking the active conformation

Grzela¹,

Nusbaum²,

Fieulaine³

et al. 2017

Sci Rep

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Prokaryotic proteins must be deformylated before the removal of their first methionine. Peptide deformylase (PDF) is indispensable and guarantees this mechanism. Recent metagenomics studies revealed new idiosyncratic PDF forms as the most abundant family of viral sequences. Little is known regarding these viral PDFs, including the capacity of the corresponding encoded proteins to ensure deformylase activity. We provide here the first evidence that viral PDFs, including the shortest PDF identified to date, Vp16 PDF, display deformylase activity in vivo, despite the absence of the key ribosome-interacting C-terminal region. Moreover, characterization of phage Vp16 PDF underscores unexpected structural and molecular features with the C-terminal Isoleucine residue significantly contributing to deformylase activity both in vitro and in vivo. This residue fully compensates for the absence of the usual long C-domain. Taken together, these data elucidate an unexpected mechanism of enzyme natural evolution and adaptation within viral sequences.

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“…While solution-state NMR and X-ray crystallography was widely used on small viral membrane proteins in detergent, solid-state NMR has the advantage that the proteins can be investigated in lipids, which are closer mimics of native membranes. Solid-state NMR investigations were first initiated on small viral membrane proteins, also called “viral membrane-spanning mini-proteins” [ 117 ], often using oriented samples to obtain spectra [ 118 ]. In this context, HIV-1, influenza and parainfluenza virus fusion peptides of ~20 amino acids have been studied early on [ 119 , 120 , 121 , 122 ] to reveal the structure and orientation behavior of these fragments in lipid bilayers under conditions mimicking membrane fusion.…”

Section: Examples Of Solid-state Nmr Studies On Viral Proteinsmentioning

confidence: 99%

Solid-State NMR for Studying the Structure and Dynamics of Viral Assemblies

Lecoq

Fogeron

Meier

et al. 2020

Viruses

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Structural virology reveals the architecture underlying infection. While notably electron microscopy images have provided an atomic view on viruses which profoundly changed our understanding of these assemblies incapable of independent life, spectroscopic techniques like NMR enter the field with their strengths in detailed conformational analysis and investigation of dynamic behavior. Typically, the large assemblies represented by viral particles fall in the regime of biological high-resolution solid-state NMR, able to follow with high sensitivity the path of the viral proteins through their interactions and maturation steps during the viral life cycle. We here trace the way from first solid-state NMR investigations to the state-of-the-art approaches currently developing, including applications focused on HIV, HBV, HCV and influenza, and an outlook to the possibilities opening in the coming years.

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Relating structure and function of viral membrane-spanning miniproteins

Cited by 20 publications

References 58 publications

Interactions of SARS-CoV-2 envelope protein with amilorides correlate with antiviral activity

Interactions of SARS-CoV-2 envelope protein with amilorides correlate with antiviral activity

The C-terminal residue of phage Vp16 PDF, the smallest peptide deformylase, acts as an offset element locking the active conformation

Solid-State NMR for Studying the Structure and Dynamics of Viral Assemblies

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