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

Abstract

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.

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

“…The prepared LUVs were stored at 4 o C and used within seven days. Detailed protocols have been reported previously [39,41,47]. preprint (which was not certified by peer review) is the author/funder.…”

“…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].…”

“…The E-CTD contains the highly conserved cysteine-containing motif CxxC that may allow disulfide isomerization to enhance membrane-directed conformational changes [19]. Moreover, it contains different potent glycosylation sites essential for maintaining the protein broad functional roles and may act as chaperone interacting motifs to help in the protein folding [8,17,41]. The PDZ-binding domain (PBM) motif DLLV at the end of E-CTD plays a crucial role in host cell modifications required for viral infection and pathogenesis [8,24].…”

“…We also observed a transition from 0 M TMAO to 2. in the presence of TMAO [37][38][39]. However, some IDPs exhibit a different behaviour [40,41], as they only exhibit a reduction in negative ellipticity at 198-202 nm. Overall, these results indicate that the E-CTD in the presence of TMAO undergoes a transition from disorder to ordered (Figure 9).…”

“…As no structure is currently available for the E-CTD, initial models were generated using the PepFold web server using 200 simulations of energy minimization. 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].…”