scholarly journals Sequence and Structural Analysis of COVID-19 E and M Protein With MERS Virus E and M Protein – A Comparative Study

2020 ◽  
Author(s):  
Ebtisam A. Aldaais ◽  
Subha Yegnaswamy ◽  
Fatimah Albahrani ◽  
Fatima Alsowaiket ◽  
Sarah Alramadan
Keyword(s):  
Serine Proteases ◽  
Protein A ◽  
Phosphorylation Site ◽  
Catalytic Triad ◽  
Serine Phosphorylation ◽  
M Protein ◽  
E Proteins ◽  
Structural Part ◽  
E Protein ◽  
Membrane Envelope

Abstract The outbreak of SARS in 2003, MERS in 2012, and now COVID-19 in 2019 have demonstrated that Coronaviruses are capable of causing primary lethal infections in humans, and the pandemic is now a global concern. The COVID-19 belongs to the beta coronavirus family encoding 29 proteins, of which 4 are structural, the Spike, Membrane, Envelope, and Nucleocapsid proteins. Here we have analyzed and compared the Membrane (M) and Envelope (E) proteins of COVID-19 and MERS with SARS and Bat viruses. The sequence analysis of conserved regions of both E and M protein revealed that many regions of COVID-19 are similar to Bat and SARS viruses while the MERS virus showed variations. The essential binding motifs found in SARS-CoV appeared in COVID-19. Besides, the M protein of COVID- 19 showed a distinct serine phosphorylation site in the C-terminal domain, which looked like a catalytic triad seen in serine proteases. A Dileucine motif occurred many times in the sequence of the M protein of all the four viruses compared. Concerning the structural part, the COVID-19 E protein showed more similarity to Bat while MERS shared similarity with the SARS virus. The M protein of both COVID-19 and MERS displayed variations in the structure. The interaction between M and E protein was also studied to know the additional binding regions. Our study highlights the critical motifs and structural regions to be considered for further research to design better inhibitors for the infection caused by these viruses.

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 Envelope Protein Palmitoylations Are Crucial for Murine Coronavirus Assembly

2008 ◽  
Vol 82 (6) ◽  
pp. 2989-2999 ◽  
Author(s):  
Joseph A. Boscarino ◽  
Hillary L. Logan ◽  
Jason J. Lacny ◽  
Thomas M. Gallagher
Keyword(s):  
Envelope Protein ◽  
Culture Medium ◽  
Lipid Vesicles ◽  
M Protein ◽  
Assembly Process ◽  
E Proteins ◽  
Protein Subunits ◽  
E Protein ◽  
Morphogenetic Protein ◽  
M Proteins

ABSTRACT The coronavirus assembly process encloses a ribonucleoprotein genome into vesicles containing the lipid-embedded proteins S (spike), E (envelope), and M (membrane). This process depends on interactions with membranes that may involve palmitoylation, a common posttranslational lipidation of cysteine residues. To determine whether specific palmitoylations influence coronavirus assembly, we introduced plasmid DNAs encoding mouse hepatitis coronavirus (MHV) S, E, M, and N (nucleocapsid) into 293T cells and found that virus-like particles (VLPs) were robustly assembled and secreted into culture medium. Palmitate adducts predicted on cysteines 40, 44, and 47 of the 83-residue E protein were then evaluated by constructing mutant cDNAs with alanine or glycine codon substitutions at one or more of these positions. Triple-substituted proteins (E.Ts) lacked palmitate adducts. Both native E and E.T proteins localized at identical perinuclear locations, and both copurified with M proteins, but E.T was entirely incompetent for VLP production. In the presence of the E.T proteins, the M protein subunits accumulated into detergent-insoluble complexes that failed to secrete from cells, while native E proteins mobilized M into detergent-soluble secreted forms. Many of these observations were corroborated in the context of natural MHV infections, with native E, but not E.T, complementing debilitated recombinant MHVs lacking E. Our findings suggest that palmitoylations are essential for E to act as a vesicle morphogenetic protein and further argue that palmitoylated E proteins operate by allowing the primary coronavirus assembly subunits to assume configurations that can mobilize into secreted lipid vesicles and virions.

Chapter 2b: The molecular antigenic structure of the TBEV

2020 ◽  
Keyword(s):  
Conformational Changes ◽  
Neutralizing Antibodies ◽  
Lipid Membrane ◽  
Cell Entry ◽  
Antigenic Structure ◽  
E Proteins ◽  
Amino Acid Sequence Level ◽  
Endosomal Membrane ◽  
E Protein ◽  
Golgi Network

TBEV-particles are assembled in an immature, noninfectious form in the endoplasmic reticulum by the envelopment of the viral core (containing the viral RNA) by a lipid membrane associated with two viral proteins, prM and E. Immature particles are transported through the cellular exocytic pathway and conformational changes induced by acidic pH in the trans-Golgi network allow the proteolytic cleavage of prM by furin, a cellular protease, resulting in the release of mature and infectious TBE-virions. The E protein controls cell entry by mediating attachment to as yet ill-defined receptors as well as by low-pH-triggered fusion of the viral and endosomal membrane after uptake by receptor-mediated endocytosis. Because of its key functions in cell entry, the E protein is the primary target of virus neutralizing antibodies, which inhibit these functions by different mechanisms. Although all flavivirus E proteins have a similar overall structure, divergence at the amino acid sequence level is up to 60 percent (e.g. between TBE and dengue viruses), and therefore cross-neutralization as well as (some degree of) cross-protection are limited to relatively closely related flaviviruses, such as those constituting the tick-borne encephalitis serocomplex.

scholarly journals Co-relation with novel phosphorylation sites of IκBα and necroptosis in breast cancer cells

BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Sung Hoon Choi ◽  
Hee-Sub Yoon ◽  
Shin-Ae Yoo ◽  
Sung Ho Yun ◽  
Joo-Hee Park ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Cancer Cells ◽  
Breast Cancer Cells ◽  
Phosphorylation Site ◽  
Aurora Kinase ◽  
Serine Phosphorylation ◽  
Flight Mass Spectrometry ◽  
Iκb Kinase ◽  
Orbitrap Mass Spectrometer ◽  
Nf Kappab

Abstract Background Phosphorylation of NF-kappaB inhibitor alpha (IκBα) is key to regulation of NF-κB transcription factor activity in the cell. Several sites of IκBα phosphorylation by members of the IκB kinase family have been identified, but phosphorylation of the protein by other kinases remains poorly understood. We investigated a new phosphorylation site on IκBα and identified its biological function in breast cancer cells. Methods Previously, we observed that aurora kinase (AURK) binds IκBα in the cell. To identify the domains of IκBα essential for phosphorylation by AURK, we performed kinase assays with a series of IκBα truncation mutants. AURK significantly promoted activation of IκBα at serine 32 but not serine 36; by contrast, IκB kinase (IKK) family proteins activated both of these residues. We also confirmed phosphorylation of IκBα by matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/TOF MS) and nano-liquid chromatography hybrid quadrupole orbitrap mass spectrometer (nanoLC-MS/MS; Q-Exactive). Results We identified two novel sites of serine phosphorylation, S63 and S262. Alanine substitution of S63 and S262 (S63A and S262A) of IκBα inhibited proliferation and suppressed p65 transcription activity. In addition, S63A and/or S262A of IκBα regulated apoptotic and necroptotic effects in breast cancer cells. Conclusions Phosphorylation of IκBα by AURK at novel sites is related to the apoptosis and necroptosis pathways in breast cancer cells.

scholarly journals Increased oncogenic potential of ErbB is associated with the loss of a COOH-terminal domain serine phosphorylation site.

1992 ◽  
Vol 267 (12) ◽  
pp. 7967-7970
Author(s):  
S.J. Theroux ◽  
C Taglienti-Sian ◽  
N Nair ◽  
J.L. Countaway ◽  
H.L. Robinson ◽  
...  
Keyword(s):  
Phosphorylation Site ◽  
Serine Phosphorylation ◽  
Oncogenic Potential ◽  
Terminal Domain

scholarly journals The Actin-Binding Protein UNC-115/abLIM Controls Formation of Lamellipodia and Filopodia and Neuronal Morphogenesis in Caenorhabditis elegans

2005 ◽  
Vol 25 (12) ◽  
pp. 5158-5170 ◽  
Author(s):  
Yieyie Yang ◽  
Erik A. Lundquist
Keyword(s):  
Caenorhabditis Elegans ◽  
Molecular Mechanisms ◽  
Binding Protein ◽  
Phosphorylation Site ◽  
Serine Phosphorylation ◽  
Actin Binding ◽  
Axon Pathfinding ◽  
Neuronal Morphogenesis ◽  
Actin Binding Protein ◽  
C Elegans

ABSTRACT The roles of actin-binding proteins in development and morphogenesis are not well understood. The actin-binding protein UNC-115 has been implicated in cytoskeletal signaling downstream of Rac in Caenorhabditis elegans axon pathfinding, but the cellular role of UNC-115 in this process remains undefined. Here we report that UNC-115 overactivity in C. elegans neurons promotes the formation of neurites and lamellipodial and filopodial extensions similar to those induced by activated Rac and normally found in C. elegans growth cones. We show that UNC-115 activity in neuronal morphogenesis is enhanced by two molecular mechanisms: when ectopically driven to the plasma membrane by the myristoylation sequence of c-Src, and by mutation of a putative serine phosphorylation site in the actin-binding domain of UNC-115. In support of the hypothesis that UNC-115 modulates actin cytoskeletal organization, we show that UNC-115 activity in serum-starved NIH 3T3 fibroblasts results in the formation of lamellipodia and filopodia. We conclude that UNC-115 is a novel regulator of the formation of lamellipodia and filopodia in neurons, possibly in the growth cone during axon pathfinding.

Characterization of CAP1 and ECA4 adaptors participating in clathrin-mediated endocytosis

2022 ◽  
Author(s):  
Maciek Adamowski ◽  
Ivana Matijević ◽  
Jiří Friml
Keyword(s):  
Fluorescent Protein ◽  
Phosphorylation Site ◽  
Large Family ◽  
Adaptor Proteins ◽  
Serine Phosphorylation ◽  
Binding Motif ◽  
Double Knockout ◽  
Coated Pits ◽  
Knockout Mutants ◽  
Golgi Network

Formation of endomembrane vesicles is crucial in all eukaryotic cells and relies on vesicle coats such as clathrin. Clathrin-coated vesicles form at the plasma membrane and the trans-Golgi Network. They contain adaptor proteins, which serve as binding bridges between clathrin, vesicle membranes, and cargoes. A large family of monomeric ANTH/ENTH/VHS adaptors is present in A. thaliana. Here, we characterize two homologous ANTH-type clathrin adaptors, CAP1 and ECA4, in clathrin-mediated endocytosis (CME). CAP1 and ECA4 are recruited to sites at the PM identified as clathrin-coated pits (CCPs), where they occasionally exhibit early bursts of high recruitment. Subcellular binding preferences of N- and C-terminal fluorescent protein fusions of CAP1 identified a functional adaptin-binding motif in the unstructured tails of CAP1 and ECA4. In turn, no function can be ascribed to a double serine phosphorylation site conserved in these proteins. Double knockout mutants do not exhibit deficiencies in general development or CME, but a contribution of CAP1 and ECA4 to these processes is revealed in crosses into sensitized endocytic mutant backgrounds. Overall, our study documents a contribution of CAP1 and ECA4 to CME in A. thaliana and opens questions about functional redundancy among non-homologous vesicle coat components.

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