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Dengue viruses are human pathogens that are transmitted through mosquitoes. Apart from the typical symptoms associated with viral fevers, DENV infections are known to cause several neurological complications such as meningitis, encephalitis, intracranial haemorrhage, retinopathies along with the more severe, and sometimes fatal, vascular leakage and dengue shock syndrome. This study was designed to investigate, in detail, the predicted viral protein aggregation prone regions among all serotypes. Further, in order to understand the cross-talk between viral protein aggregation and aggregation of cellular proteins, cross-seeding experiments between the DENV NS1 (1-30), corresponding to the β-roll domain and the diabetes hallmark protein, amylin, were performed. Various techniques such as fluorescence spectroscopy, circular dichroism, atomic force microscopy and immunoblotting have been employed for this. We observe that the DENV proteomes have many predicted APRs and the NS1 (1-30) of DENV1-3, 2K and capsid anchor of DENV2 and DENV4 are capable of forming amyloids, in vitro. Further, the DENV NS1 (1-30), aggregates are also able to cross-seed and enhance amylin aggregation and vice-versa. This knowledge may lead to an opportunity for designing suitable inhibitors of protein aggregation that may be beneficial for viral infections and comorbidities. highlighting the questions asked and the observations made in the current manuscript. Amyloid formation by the DENV peptides, NS1 (1-30), 2K and capsid anchor was observed. Further, the aggregation of NS1 (1-30), could cross-seed and enhance the aggregation of human amylin and vice-versa. [Display omitted] • We've predicted the aggregation prone regions in the proteomes of the four DENV (1-4) serotypes using four online predictors. • NS1 (1-30) of DENV1-3 and the 2K and CA peptides of DENV2 and DENV4 are capable of aggregating and forming amyloid structures in vitro under physiological conditions, shown through various techniques such as fluorescence spectroscopy, circular dichroism, atomic force microscopy and immunoblotting • NS1 (1-30) aggregates also interact with the human amylin and cross-seed and enhance its aggregation and vice-versa. • We hypothesize that the pathogenicity of DENV infection could be a function of viral protein aggregation and that the adversity of symptoms observed in diabetic dengue patients could be due to the cross-talk between the aggregation pathways of both the DENV and diabetes systems. [ABSTRACT FROM AUTHOR]

Capsid-anchor (CA) of Zika virus (ZIKV) is a small, single-pass transmembrane sequence that separates the capsid (C) protein from downstream pre-membrane (PrM) protein. During polyprotein processing, CA is cleaved-off from C and PrM and left as a membrane-embedded peptide. CA plays an essential role in the assembly and maturation of the virus. However, its independent folding behavior is still unknown. Therefore, in this study, we investigated the amyloid-forming propensity of CA at physiological conditions. We observed the aggregation behavior of CA peptide using dye-binding assays and ThT kinetics. The morphological analysis of CA aggregates explored by high-resolution microscopy (TEM, AFM) and Far-UV CD spectroscopy revealed characteristic amyloid-like fibrils rich in β-sheet secondary structure. Further, the effect on mammalian cells exhibited the cytotoxic nature of the CA amyloid-fibrils. Our findings collectively shed light on the amyloidogenic phenomenon of flaviviral protein, which may contribute to their infection. Schematic representation of Zika virus Capsid anchor forming amyloid aggregates with cytotoxic and hemolytic properties. [Display omitted] • Residues 6th-17th of Zika virus Capsid anchor are predicted amyloid prone region (APR). • Amyloid specific dye-binding assays revealed CA kinetics with shorter initiation phase. • Morphological analysis of aggregates by TEM and AFM revealed characteristic amyloid-like fibrils. • CD spectra of Capsid anchor transitions from disordered/random coil conformation to amyloid fibril specific beta-sheet. • CD spectra of Capsid anchor transitions from disordered/random coil conformation to amyloid fibril specific beta-sheet. • Effect of CA aggregates on mammalian cells and RBCs suggests their cytotoxic and membrane damaging nature. [ABSTRACT FROM AUTHOR]

Japanese encephalitis virus (JEV) is one of the major causes of viral encephalitis all around the globe. Approximately 3 billion people in endemic areas are at risk of Japanese encephalitis. To develop a wholistic understanding of the viral proteome, it is important to investigate both its ordered and disordered proteins. However, the functional and structural significance of disordered regions in the JEV proteome has not been systematically investigated as of yet. To fill this gap, we used here a set of bioinformatics tools to analyze the JEV proteome for the predisposition of its proteins for intrinsic disorder and for the presence of the disorder‐based binding regions (also known as molecular recognition features, MoRFs). We also analyzed all JEV proteins for the presence of the probable nucleic acid‐binding (DNA and RNA) sites. The results of these computational studies are experimentally validated using JEV capsid protein as an illustrative example. In agreement with bioinformatic analysis, we found that the N‐terminal region of the JEV capsid (residues 1–30) is intrinsically disordered. We showed that this region is characterized by the temperature response typical for highly disordered proteins. Furthermore, we have experimentally shown that this disordered N‐terminal domain of a capsid protein has a noticeable 'gain‐of‐structure' potential. In addition, using DOPS liposomes, we demonstrated the presence of pronounced membrane‐mediated conformational changes in the N‐terminal region of JEV capsid. In our view, this disorder‐centric analysis would be helpful for a better understanding of the JEV pathogenesis. [ABSTRACT FROM AUTHOR]

4H-Chromene derivatives are promising anticancer compounds known to bind within the colchicine binding site of the tubulin protein. Among these, the 2-amino-4-phenyl-4H-benzo[h]chromene-3-carbonitrile-based 4H-chromenes scaffold is known to produce a significant impact on tubulin proteins. Other molecules with similar pharmacophores are also known for their colchicine binding site targeting abilities. However, tubulin is not a single protein; multiple isoforms have been reported, and some are comparatively more important under malignant conditions. Therefore, the research findings presented herein include a detailed understanding of the interaction pattern of the 2-amino-4-phenyl-4H-benzo[h]chromene-3-carbonitrile series for their colchicine binding ability against various tubulin isoforms proteins. We have established the current series anticancer potential and structural activity relationship. The series revealed promising anticancer potential, and MNC-1 was the best among all. However, a serious side effect of this scaffold is a major problem, as these derivatives indiscriminately bind to the tubulin of malignant and normal cells. However, the expression profile of tubulin isoforms was found to be different in normal and malignant cell types. Therefore, selective killing of the malignant cell seems possible by designing a 4H-chromenes derivative selective against particular tubulin isoforms. The insights provided herein clearly indicate the differences in the binding pattern of different 4H-chromenes derivatives against different tubulin isoforms. Therefore, with precise structural modification, these molecules' selective targeting against cancer cells seems quite possible. [ABSTRACT FROM AUTHOR]

Zika virus capsid protein is involved in multiple essential steps of the viral life cycle. Many vital functionalities are attributed to the dynamic N- terminal domain of this protein, which is intrinsically disordered in ZIKV and among several flaviviruses too. Other than genome encapsulation, studies have shown interaction with host lipid droplets to be crucial for replication and maturation. In Dengue virus, the molecular basis of such interplay has been studied in detail, and residues within the capsid N-terminal disordered domain has been mapped. It revealed a new function of a conserved region in mediating capsid-lipid droplet association through a conformational transition. Therefore, in this study, we attempt to analyze the structural dynamics of Zika virus capsid's N- terminal domain and analyzed it through a reductionist approach by dividing the N-terminal domain into three truncated segments and studied them individually. Techniques such as Circular dichroism spectroscopy, Dynamic light scattering, Zeta potential and Molecular dynamic simulations were employed to identify the motif responsible for structural flexibility and ability to interact with membrane models. Our results confirm that the truncated segments 5–26 and 1–30 readily adopt an α -helical conformation in the presence of 2,2,2-trifluoro-ethanol, detergent and negatively charged phospholipids. However, in contrast to Dengue virus, we report the conserved residues 14–23 region to be unstructured and do not undergo a conformational switch in Zika virus. Thus, our study illustrates the possibility of conserved 14–23 region's non-involvement in ZIKV capsid-lipid droplet association, unlike DENV. Unlabelled Image • Capsid N-terminal regions 1-30 and 5-26, undergo disorder-to-order transition in the presence of TFE, SDS and liposomes. • The conserved region (14-23) of ZIKV-C does not undergo any conformational change. • Unlike DENV, the 14-23 conserved region may not be involved in the lipid interactions in ZIKV-C. • The lipid interacting motif of ZIKV-C N-terminal may span the region between residues 24-30. [ABSTRACT FROM AUTHOR]

The NSP6 protein of SARS-CoV-2 is a transmembrane protein, with some regions lying outside the membrane. Besides a brief role of NSP6 in autophagosome formation, this is not studied significantly. Also, there is no structural information available to date. Based on the prediction by TMHMM server for transmembrane prediction, it is found that the N-terminal residues (1-11), middle region residues (91–112), and C-terminal residues (231–290) lies outside the membrane. Molecular Dynamics (MD) simulations showed that NSP6 consists of helical structures. In contrast, the membrane outside lying region (91–112) showed partial helicity, which was further used as a model and obtained disordered type conformation during 1.5 μs. Additionally, a 200ns simulation study of residues 231–290 have shown significant conformational changes. As compared to helical and beta-sheet conformations in its structure model, the 200ns simulation resulted in the loss of beta-sheet structures while helical regions remained intact. Further, we have experimentally characterized the residue 91–112 by using reductionist approaches. CD spectroscopy suggests that the NSP6 (91–112) is disordered-like region in isolation, which gains helical conformation in different biological mimic environmental conditions. These studies can be helpful to study NSP6 (91–112) interactions with host proteins, where different protein conformations might play a significant role. The present study adds up more information about the NSP6 protein aspect, which could be exploited for its host protein interaction and pathogenesis. The schematic representation of NSP6 membrane topology and conformational dynamics of residue 91–112. The N-terminal and C-terminal are shown in cytoplasmic side based on the experimental evidence on coronaviruses reported by Oostra et al., 2008. The membrane anchoring domain are shown based on the TMHMM server prediction. [Display omitted] • MD simulations study of SARS-CoV-2 NSP6 model is conducted to reveal its dynamics due to unavailability of its 3D structure. • Transmembrane regions are predicted using TMHMM web-server which predicted seven transmembrane regions. • Two non-transmembrane regions (residues 91–112 and 231–290) are investigated through extensive MD simulations. • NSP6 (91–112) region is investigated for its structural conformations using CD spectroscopy and fluorescence spectroscopy. [ABSTRACT FROM AUTHOR]