scholarly journals Structure and dynamics of the SARS-CoV-2 envelope protein monomer

2021 ◽  
Author(s):  
Alexander Kuzmin ◽  
Philipp Orekhov ◽  
Roman Astashkin ◽  
Valentin Gordeliy ◽  
Ivan Gushchin
Keyword(s):  
Envelope Protein ◽  
Transmembrane Domain ◽  
Membrane Surface ◽  
Protein A ◽  
Membrane Curvature ◽  
Curvature Sensing ◽  
Structure And Dynamics ◽  
E Protein ◽  
Viral Particles ◽  
Dynamics Simulations

AbstractCoronaviruses, especially SARS-CoV-2, present an ongoing threat for human wellbeing. Consequently, elucidation of molecular determinants of their function and interaction with host is an important task. Whereas some of the coronaviral proteins are extensively characterized, others remain understudied. Here, we use molecular dynamics simulations to analyze the structure and dynamics of the SARS-CoV-2 envelope protein (E protein, a viroporin) in the monomeric form. The protein consists of three parts: hydrophobic α-helical transmembrane domain (TMD) and amphiphilic α-helices H2 and H3, which are connected by flexible linkers. We show that TMD is tilted in the membrane, with phenylalanines Phe20, Phe23 and Phe26 facing the lumen. H2 and H3 reside at the membrane surface. Orientation of H2 is not affected by glycosylation, but strongly influenced by palmitoylation pattern of cysteines Cys40, Cys43 and Cys44. On the other hand, glycosylation affects the orientation of H3 and prevents its stacking with H2. We also find that the E protein both generates and senses the membrane curvature, preferably localizing with the cytoplasmic part at the convex regions of the membrane. Curvature sensing may be favorable for assembly of the E protein oligomers, whereas induction of curvature may facilitate budding of the viral particles. The presented results may be helpful for better understanding of the function of coronaviral E protein and viroporins in general, and for overcoming the ongoing SARS-CoV-2 pandemic.

scholarly journals Influenza hemagglutinin drives viral entry via two sequential intramembrane mechanisms

2020 ◽  
Author(s):  
Anna Pabis ◽  
Robert J. Rawle ◽  
Peter M. Kasson
Keyword(s):  
Viral Entry ◽  
Transmembrane Domain ◽  
Critical Role ◽  
Cellular Membrane ◽  
Membrane Curvature ◽  
Viral Envelope ◽  
Enveloped Viruses ◽  
Influenza Hemagglutinin ◽  
Hemagglutinin Protein ◽  
Dynamics Simulations

AbstractEnveloped viruses enter cells via a process of membrane fusion between the viral envelope and a cellular membrane. For influenza virus, mutational data have shown that the membrane-inserted portions of the hemagglutinin protein play a critical role in achieving fusion. In contrast to the relatively well-understood ectodomain, a predictive mechanistic understanding of the intramembrane mechanisms by which influenza hemagglutinin drives fusion has been elusive. We have used molecular dynamics simulations of fusion between a full-length hemagglutinin proteoliposome and a lipid bilayer to analyze these mechanisms. In our simulations, hemagglutinin first acts within the membrane to increase lipid tail protrusion and promote stalk formation and then acts to engage the distal leaflets of each membrane and promote stalk widening, curvature, and eventual fusion. These two sequential mechanisms, one occurring prior to stalk formation and one after, are consistent with experimental measurements we report of single-virus fusion kinetics to liposomes of different sizes. The resulting model also helps explain and integrate prior mutational and biophysical data, particularly the mutational sensitivity of the fusion peptide N-terminus and the length sensitivity of the transmembrane domain. We hypothesize that entry by other enveloped viruses may also utilize sequential processes of acyl tail exposure followed by membrane curvature and distal leaflet engagement.

scholarly journals Virtual Repurposing of Ursodeoxycholate and Chenodeoxycholate as Lead Candidates Against SARS-Cov2-Envelope Protein: A Molecular Dynamics Investigation

2020 ◽  
Author(s):  
Reena Yadav ◽  
chinmayee choudhury ◽  
Yashwant Kumar ◽  
Alka Bhatia
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamics Simulations ◽  
Envelope Protein ◽  
Homology Modelling ◽  
Protein A ◽  
Drug Repurposing ◽  
Dynamics Simulations ◽  
Global Threat ◽  
Polar Functional Groups

Drug repurposing is an apt choice to combat the currently prevailing global threat of COVID-19, caused by SARS-Cov2 in absence of any specific medication/vaccine. The present work attempts to computationally evaluate binding affinities and effect of two widely used surfactant drugs i.e. chenodeoxycholate (CDC) and ursodeoxycholate (UDC) with the envelope protein of SARS-Cov2 (SARS-Cov2-E) using homology modelling, molecular docking and molecular dynamics simulations. A good quality homo-pentameric structure of SARS-Cov2-E was modelled from its homologue with more than 90% sequence identity followed by symmetric docking. The pentameric structure was embedded in a DPPC membrane and subsequently energy minimized. The minimized structure was used for blind molecular docking of CDC and UDC to obtain the best scoring SARS-Cov2-E–CDC/UDC complexes, which were subjected to 230ns molecular dynamics simulations in triplicates in DPPC membrane environment. Comparative analyses of structural and enthalpic properties and molecular interaction profiles from the MD trajectories revealed that, both CDC and UDC could stably bind to SARS-Cov2-E through H-bonds, water-bridges and hydrophobic contacts in the transmembraneresidues.T30 was observed to be a key residue for CDC/UDC binding. The polar functional groups of the bound CDC/UDC facilitated entry of a large number of water molecules into the channel and affected the H-bonding pattern between adjacent monomeric chains, loosening the compact transmembrane region of SARS-Cov2-E. These observations suggest the potential of CDC/UDC as repurposed candidates to hinder the survival of SARS-Cov2 by disrupting the structure of SARS-Cov2-E and facilitate entry of solvents/polar inhibitors inside the viral cell.

scholarly journals Clustering and dynamics of crowded proteins near membranes and their influence on membrane bending

2019 ◽  
Vol 116 (49) ◽  
pp. 24562-24567 ◽  
Author(s):  
Grzegorz Nawrocki ◽  
Wonpil Im ◽  
Yuji Sugita ◽  
Michael Feig
Keyword(s):  
Membrane Surface ◽  
Membrane Curvature ◽  
Phospholipid Bilayer ◽  
Protein Solutions ◽  
Protein Diffusion ◽  
Depletion Zone ◽  
Head Groups ◽  
Membrane Contacts ◽  
Membrane Bending ◽  
Dynamics Simulations

Atomistic molecular dynamics simulations of concentrated protein solutions in the presence of a phospholipid bilayer are presented to gain insights into the dynamics and interactions at the cytosol–membrane interface. The main finding is that proteins that are not known to specifically interact with membranes are preferentially excluded from the membrane, leaving a depletion zone near the membrane surface. As a consequence, effective protein concentrations increase, leading to increased protein contacts and clustering, whereas protein diffusion becomes faster near the membrane for proteins that do occasionally enter the depletion zone. Since protein–membrane contacts are infrequent and short-lived in this study, the structure of the lipid bilayer remains largely unaffected by the crowded protein solution, but when proteins do contact lipid head groups, small but statistically significant local membrane curvature is induced, on average.

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

2021 ◽  
Author(s):  
Sang Ho Park ◽  
Haley Siddiqi ◽  
Daniela V. Castro ◽  
Anna De Angelis ◽  
Aaron L. Oom ◽  
...  
Keyword(s):  
Drug Discovery ◽  
Chemical Shift ◽  
Antiviral Activity ◽  
Viral Replication ◽  
Binding Site ◽  
Transmembrane Domain ◽  
The Novel ◽  
Structure And Dynamics ◽  
E Protein ◽  
Novel Coronavirus

AbstractSARS-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.Author SummaryThe novel coronavirus SARS-CoV-2, the causative agent of the world-wide pandemic of COVID-19, has become one of the greatest threats to human health. While rapid progress has been made in the development of vaccines, drug discovery has lagged, partly due to the lack of atomic-resolution structures of the free and drug-bound forms of the viral proteins. The SARS-CoV-2 envelope (E) protein, with its multiple activities that contribute to viral replication, is widely regarded as a potential target for COVID-19 treatment. As structural information is essential for drug discovery, we established an efficient sample preparation system for biochemical and structural studies of intact full-length SARS-CoV-2 E protein and characterized its structure and dynamics. We also characterized the interactions of amilorides with specific E protein residues and correlated this with their antiviral activity during viral replication. The binding affinity of the amilorides to E protein correlated with their antiviral potency, suggesting that E protein is indeed the likely target of their antiviral activity. We found that residue asparagine15 plays an important role in maintaining the conformation of the amiloride binding site, providing molecular guidance for the design of inhibitors targeting E protein.

Dynamics of Membrane-Embedded Lipid-Linked Oligosaccharides for the Three Domains of Life

2019 ◽  
Author(s):  
Pablo Ricardo Arantes ◽  
Conrado Pedebos ◽  
Laércio Pol-Fachin ◽  
Marcelo D. Poleto ◽  
Hugo Verli
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Membrane Surface ◽  
Membrane Lipid ◽  
Head Group ◽  
En Bloc ◽  
Structure And Dynamics ◽  
Domains Of Life ◽  
Dynamics Simulations ◽  
Orientation Structure

<div>Lipid-linked oligosaccharides (LLOs) are the substrates of oligosaccharyltransferases (OSTs), enzymes that catalyze the en bloc transfer of a glycan chain during the process of N-glycosylation. LLOs are composed by an isoprenoid chain moiety and an oligosaccharide, linked by one or more pyrophosphate groups (PP). The lipid component on LLO is a dolichol in eukarya and archaea, and an undecaprenol in prokarya, whereas the number of isoprene units may change between species. Given the potential relevance of LLOs and their metabolizing enzymes to diverse biotechnological applications, LLOs’ models from different domains of life in their native conditions could support further studies of their complexation and processing by OSTs, as well as protein engineering on such systems. Accordingly, the GROMOS53A6 force field was employed, added by GROMOS53a6GLYC parameters for the saccharidic moiety. The torsional parameters for the isoprenoid portion were derived from a fit to the proper quantum mechanical potential energy profiles at the HF 6-31G* and validated against experimental condensed phase properties. Molecular dynamics simulations employed GROMACS package to access the orientation, structure, and dynamics of eukaryotic (Glc3-Man9-GlcNAc2-PP-Dolichol), bacterial (Glc1-GalNAc5-Bac1-PP-Undecaprenol) and archaeal (Glc1-Man1-Gal1-Man1-Glc1-Gal1-Glc1-P-Dolichol) LLO in membrane bilayers. Microsecond molecular dynamics simulations of LLOs revealed that most carbohydrate residues interact with the membrane lipid head groups, parallel to the membrane surface, while the PP linkages are within the lipid head group, and the isoprenoid chains are within the bilayer. Overall, there are similarities in the orientations, structure, and dynamics of the eukaryotic, bacterial and archaea LLOs in bilayers. LLOs’ preferred orientation, structure and dynamics provided information for complexation with OSTs, allowing further studies of how these enzymes catalyze the transfer of the oligosaccharide chain to an acceptor protein by OSTs.</div>

scholarly journals Curvature–undulation coupling as a basis for curvature sensing and generation in bilayer membranes

2016 ◽  
Vol 113 (35) ◽  
pp. E5117-E5124 ◽  
Author(s):  
Ryan P. Bradley ◽  
Ravi Radhakrishnan
Keyword(s):  
Objective Function ◽  
Protein Localization ◽  
Membrane Curvature ◽  
Coarse Grained ◽  
Spontaneous Curvature ◽  
Curvature Sensing ◽  
Cooperative Process ◽  
Dynamics Simulations ◽  
A Site ◽  
Dilute Limit

We present coarse-grained molecular dynamics simulations of the epsin N-terminal homology domain interacting with a lipid bilayer and demonstrate a rigorous theoretical formalism and analysis method for computing the induced curvature field in varying concentrations of the protein in the dilute limit. Our theory is based on the description of the height–height undulation spectrum in the presence of a curvature field. We formulated an objective function to compare the acquired undulation spectrum from the simulations to that of the theory. We recover the curvature field parameters by minimizing the objective function even in the limit where the protein-induced membrane curvature is of the same order as the amplitude due to thermal undulations. The coupling between curvature and undulations leads to significant predictions: (i) Under dilute conditions, the proteins can sense a site of spontaneous curvature at distances much larger than their size; (ii) as the density of proteins increases the coupling focuses and stabilizes the curvature field to the site of the proteins; and (iii) the mapping of the protein localization and the induction of a stable curvature is a cooperative process that can be described through a Hill function.

scholarly journals Molecular Docking Analysis of Phytochemical Thymoquinone as a Therapeutic Agent on SARS-Cov-2 Envelope Protein

2020 ◽  
Vol 11 (1) ◽  
pp. 8389-8401
Keyword(s):  
Molecular Docking ◽  
Envelope Protein ◽  
Pore Formation ◽  
Transmembrane Domain ◽  
Binding Free Energy ◽  
Three Dimensional ◽  
Homology Model ◽  
Amino Terminal ◽  
E Protein ◽  
Α Helix

The sudden outbreak due to severe acute respiratory syndrome coronavirus 2 (SARS- Cov-2) is responsible for causing acute, highly dreadful coronavirus disease (COVID‐19). The pore-forming proteins in the SARS- CoV-2 envelope protein employ amphipathic α-helix for pore formation. The pore openings are essential for the transport of ions, toxins, and viroporin activity. Moreover, there is an insurgence to identify lead compounds to target the novel coronavirus for therapeutic purposes. Therefore in the present study, the SARS CoV-2 envelope protein sequence was analyzed, constructed the three-dimensional homology model, and screened against the bioactive phytochemical Thymoquinone (TQ). Molecular docking was performed between the modeled E protein and TQ to study protein-ligand interactions using ArgusLab 4.0. The investigation revealed that the modeled E protein contains a single α-amphipathic helix identified for the first time across the Amino-terminal region of the transmembrane domain may contribute to pore formation of small membrane proteins. Molecular docking results showed the promising inhibitory potential of the ligand TQ and the binding free energy of the bound complex was found to be -9.01 kcal/mol. The in silico approach has explicitly demonstrated the significant inhibitory effects of the ligand TQ. Therefore it may be used effectively as an antagonist against the SARS- CoV-2 infection owing to its outstanding pharmacological properties.

scholarly journals Virtual Repurposing of Ursodeoxycholate and Chenodeoxycholate as Lead Candidates Against SARS-Cov2-Envelope Protein: A Molecular Dynamics Investigation

2020 ◽  
Author(s):  
Reena Yadav ◽  
chinmayee choudhury ◽  
Yashwant Kumar ◽  
Alka Bhatia
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamics Simulations ◽  
Envelope Protein ◽  
Homology Modelling ◽  
Protein A ◽  
Drug Repurposing ◽  
Dynamics Simulations ◽  
Global Threat ◽  
Polar Functional Groups

Drug repurposing is an apt choice to combat the currently prevailing global threat of COVID-19, caused by SARS-Cov2 in absence of any specific medication/vaccine. The present work attempts to computationally evaluate binding affinities and effect of two widely used surfactant drugs i.e. chenodeoxycholate (CDC) and ursodeoxycholate (UDC) with the envelope protein of SARS-Cov2 (SARS-Cov2-E) using homology modelling, molecular docking and molecular dynamics simulations. A good quality homo-pentameric structure of SARS-Cov2-E was modelled from its homologue with more than 90% sequence identity followed by symmetric docking. The pentameric structure was embedded in a DPPC membrane and subsequently energy minimized. The minimized structure was used for blind molecular docking of CDC and UDC to obtain the best scoring SARS-Cov2-E–CDC/UDC complexes, which were subjected to 230ns molecular dynamics simulations in triplicates in DPPC membrane environment. Comparative analyses of structural and enthalpic properties and molecular interaction profiles from the MD trajectories revealed that, both CDC and UDC could stably bind to SARS-Cov2-E through H-bonds, water-bridges and hydrophobic contacts in the transmembraneresidues.T30 was observed to be a key residue for CDC/UDC binding. The polar functional groups of the bound CDC/UDC facilitated entry of a large number of water molecules into the channel and affected the H-bonding pattern between adjacent monomeric chains, loosening the compact transmembrane region of SARS-Cov2-E. These observations suggest the potential of CDC/UDC as repurposed candidates to hinder the survival of SARS-Cov2 by disrupting the structure of SARS-Cov2-E and facilitate entry of solvents/polar inhibitors inside the viral cell.

scholarly journals Understanding SARS-CoV-2 budding through molecular dynamics simulations of M and E protein complexes

2021 ◽  
Author(s):  
Logan Thrasher Collins ◽  
Tamer Elkholy ◽  
Shafat Mubin ◽  
Ricky Williams ◽  
Kayode Ezike ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Protein Complexes ◽  
Md Simulations ◽  
Membrane Curvature ◽  
M Protein ◽  
E Proteins ◽  
E Protein ◽  
Protein Dimers ◽  
Protein Dimer ◽  
Dynamics Simulations

SARS-CoV-2 and other coronaviruses pose a major threat to global health, yet treatment efforts have largely ignored the process of envelope assembly, a key part of the coronaviral life cycle. When expressed together, the M and E proteins are sufficient to facilitate coronavirus envelope assembly. Envelope assembly leads to budding of coronavirus particles into the ER-Golgi intermediate compartment (ERGIC) and subsequent maturation of the virus, yet the mechanisms behind the budding process remain poorly understood. Better understanding of budding may enable new types of antiviral therapies. To this end, we ran atomistic molecular dynamics (MD) simulations of SARS-CoV-2 envelope assembly using the Feig laboratory's refined structural models of the M protein dimer and E protein pentamer. Our MD simulations consisted of M protein dimers and E protein pentamers in patches of virtual ERGIC membrane. By examining how these proteins induce membrane curvature in silico, we have obtained insights around how the budding process may occur. In our simulations, M protein dimers acted cooperatively to induce membrane curvature. By contrast, E protein pentamers kept the membrane planar. These results could help guide the development of novel antiviral therapeutics which inhibit coronavirus budding.

scholarly journals Influenza hemagglutinin drives viral entry via two sequential intramembrane mechanisms

2020 ◽  
Vol 117 (13) ◽  
pp. 7200-7207 ◽  
Author(s):  
Anna Pabis ◽  
Robert J. Rawle ◽  
Peter M. Kasson
Keyword(s):  
Viral Entry ◽  
Transmembrane Domain ◽  
Critical Role ◽  
Cellular Membrane ◽  
Membrane Curvature ◽  
Viral Envelope ◽  
Enveloped Viruses ◽  
Influenza Hemagglutinin ◽  
Hemagglutinin Protein ◽  
Dynamics Simulations

Enveloped viruses enter cells via a process of membrane fusion between the viral envelope and a cellular membrane. For influenza virus, mutational data have shown that the membrane-inserted portions of the hemagglutinin protein play a critical role in achieving fusion. In contrast to the relatively well-understood ectodomain, a predictive mechanistic understanding of the intramembrane mechanisms by which influenza hemagglutinin drives fusion has been elusive. We used molecular dynamics simulations of fusion between a full-length hemagglutinin proteoliposome and a lipid bilayer to analyze these mechanisms. In our simulations, hemagglutinin first acts within the membrane to increase lipid tail protrusion and promote stalk formation and then acts to engage the distal leaflets of each membrane and promote stalk widening, curvature, and eventual fusion. These two sequential mechanisms, one occurring before stalk formation and one after, are consistent with our experimental measurements of single-virus fusion kinetics to liposomes of different sizes. The resulting model also helps explain and integrate previous mutational and biophysical data, particularly the mutational sensitivity of the fusion peptide N terminus and the length sensitivity of the transmembrane domain. We hypothesize that entry by other enveloped viruses may also use sequential processes of acyl tail exposure, followed by membrane curvature and distal leaflet engagement.

Sign in / Sign up

Export Citation Format

Share Document