Unlike dengue virus, the conserved 14–23 residues in N-terminal region of Zika virus capsid is not involved in lipid interactions

Saumya, Kumar Udit; Kumar, Deepak; Kumar, Prateek; Giri, Rajanish

doi:10.1016/j.bbamem.2020.183440

Cited by 16 publications

(15 citation statements)

References 65 publications

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“…Here, LUVs with neutral DOPC and anionic DOPS were prepared and used for CD experiments. Several IDPs are reported to bind efficiently to the DOPC and DOPS lipids and this interaction is accompanied by enhanced level of their α-helical structure [23,26,32]. In case of nsp11, the presence of DOPS and DOPC does not show any change in secondary structure conformation ( Figure 3E and 3F ).…”

Section: Resultsmentioning

confidence: 99%

“…It applies a coarse-grained (CG) forcefield and performs up to 200ns simulation runs to build an energy minimized structure. The detailed methodology has been given in our previous reports [23,24]. The resultant model was then prepared using Chimera by addition of missing hydrogens and proper parameterization of asymmetrical residues.…”

Section: Methodsmentioning

confidence: 99%

“…It applies a coarsegrained (CG) forcefield and performs up to 200ns simulation runs which generate upto 200 models. These models are clustered using OPEP (Optimized Potential for Efficient structure Prediction) and then build an energy minimized structure as used previously [23,24]. The resultant model was then prepared using Chimera by addition of missing hydrogens and proper assignment of bond orders.…”

Section: Structure Modelling and Molecular Dynamics (Md) Simulationmentioning

confidence: 99%

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Conformational Dynamics of NSP11 Peptide of SARS-CoV-2 Under Membrane Mimetics and Different Solvent Conditions

Gadhave

Kumar

et al. 2020

Preprint

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The intrinsically disordered proteins/regions (IDPs/IDPRs) are known to be responsible for multiple cellular processes and are associated with many chronic diseases. In viruses, the existence of disordered proteome is also proven and are related with its conformational dynamics inside the host. The SARS-CoV-2 virus has a large proteome, in which, structure and functions of many proteins are not known as of yet. Previously, we have investigated the dark proteome of SARS-CoV-2. However, the disorder status of non-structural protein 11 (nsp11) was not possible because of very small in size, just 13 amino acid long, and for most of the IDP predictors, the protein size should be at least 30 amino acid long. Also, the structural dynamics and function status of nsp11 was not known. Hence, we have performed extensive experimentation on nsp11. Our results, based on the Circular dichroism spectroscopy gives characteristic disordered spectrum for IDPs. Further, we investigated the conformational behaviour of nsp11 in the presence of membrane mimetic environment, alpha helix inducer, and natural osmolyte. In the presence of negatively charged and neutral liposomes, nsp11 remains disordered. However, with SDS micelle, it adopted an α-helical conformation, suggesting the helical propensity of nsp11. At the end, we again confirmed the IDP behaviour of nsp11 using molecular dynamics simulations.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Structure Modelling and Molecular Dynamics (Md) Simulationmentioning

confidence: 99%

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Conformational Dynamics of NSP11 Peptide of SARS-CoV-2 Under Membrane Mimetics and Different Solvent Conditions

Gadhave

Kumar

et al. 2020

Preprint

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“…A significant gain in negative ellipticity nearby 222 nm, and a loss of negative ellipticity around 198 nm, were observed ( Figure 10B). This type of temperature-driven structural change is known to derive from structural compaction, as observed in other disordered proteins and peptides [39,41,[43][44][45][46][47]. However, other studies on IDPs showed that disordered proteins may lose their α-helical structure with increasing temperature, suggesting that the α-helices are not solely responsible for the spectroscopic change detected by the CD spectroscopy [11].…”

Section: The E-ctd Shows a Temperature-dependent Compaction Charactermentioning

confidence: 97%

“…The starting model for the MD simulations was built and then prepared using Chimera by employing a previously described protocol [41,47]. To examine the conformational space accessible to the E-CTD, we performed all-atom MD simulations up to 1.5 µs using the Charmm36 force field [49] in Gromacs v5 [50], as reported previously [51]. In the presence of TIP3P water model, 0.15M NaCl, and solvation neutralizing counterions, the structure of the E-CTD was prepared and minimized using steepest descent method.…”

Section: Molecular Dynamic (Md) Simulationsmentioning

confidence: 99%

Environmental Dependence of the Structure of the C-terminal Domain of the SARS-CoV-2 Envelope Protein

Gadhave

Kumar

et al. 2020

Preprint

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The SARS-CoV-2 envelope protein (E) is involved in a broad spectrum of functions in the cycle of the virus, including assembly, budding, envelope formation, and pathogenesis. To enable these activities, E is likely to be capable of changing its conformation depending on environmental cues. To investigate this issue, here we characterised the structural properties of the C-terminal domain of E (E-CTD), which has been reported to interact with host cell membranes. We first studied the conformation of the E-CTD in solution, finding characteristic features of a disordered protein. By contrast, in the presence of large unilamellar vesicles and micelles, which mimic cell membranes, the E-CTD was observed to become structured. The E-CTD was also found to display conformational changes with osmolytes. Furthermore, prolonged incubation of the E-CTD under physiological conditions resulted in amyloid-like fibril formation. Taken together, these findings indicate that the E-CTD can change its conformation depending on its environment, ranging from a disordered state, to a membrane-bound folded state, and an amyloid state. Our results thus provide insight into the structural basis of the role of E in the viral infection process.HighlightsThe E-CTD of SARS-CoV-2 is intrinsically disordered in solutionThe E-CTD folds into an ordered structure in presence of membrane mimeticsThe E-CTD displays conformational changes in the presence of osmolytesProlonged incubation of the E-CTD leads to its self-assembly into amyloid-like fibrilsGraphical AbstractStructural heterogeneity of the E-CTD.The E-CTD shows a disordered secondary structure in an aqueous solution and converts into an ordered structure in the presence of membrane mimetics (neutral and negative lipids) and natural osmolytes (TMAO). Incubation at physiological condition shows typical amyloid-like fibrils. The yellow-colored structure represents a predicted structure of the E-CTD by PEP-FOLD.

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Met58 and di-acidic motif located at C-terminal region of SARS-CoV-2 ORF6 plays a crucial role in its structural conformations

Kumar,

Saumya,

Bhardwaj

et al. 2025

Biophysical Chemistry

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Unlike dengue virus, the conserved 14–23 residues in N-terminal region of Zika virus capsid is not involved in lipid interactions

Cited by 16 publications

References 65 publications

Conformational Dynamics of NSP11 Peptide of SARS-CoV-2 Under Membrane Mimetics and Different Solvent Conditions

Conformational Dynamics of NSP11 Peptide of SARS-CoV-2 Under Membrane Mimetics and Different Solvent Conditions

Environmental Dependence of the Structure of the C-terminal Domain of the SARS-CoV-2 Envelope Protein

Met58 and di-acidic motif located at C-terminal region of SARS-CoV-2 ORF6 plays a crucial role in its structural conformations

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