Search

The emergence of novel coronavirus SARS-CoV-2 is responsible for causing coronavirus disease-19 (COVID-19) imposing serious threat to global public health. Infection of SARS-CoV-2 to the host cell is characterized by direct translation of positive single stranded (+ ss) RNA to form large polyprotein polymerase 1ab (pp1ab), which acts as precursor for a number of nonstructural and structural proteins that play vital roles in replication of viral genome and biosynthesis of new virus particles. The maintenance of viral protein homeostasis is essential for continuation of viral life cycle in the host cell. To test whether the protein homeostasis of SARS-CoV-2 can be disrupted by inducing specific protein aggregation, we made an effort to examine whether the viral proteome contains any aggregation prone regions (APRs) that can be explored for inducing toxic protein aggregation specifically in viral proteins and without affecting the host cell. This curiosity leads to the identification of several (> 70) potential APRs in SARS-CoV-2 proteome. The length of the APRs ranges from 5 to 25 amino acid residues. Nearly 70% of total APRs investigated are relatively smaller and found to be in the range of 5-10 amino acids. The maximum number of ARPs (> 50) was observed in pp1ab. On the other hand, the structural proteins such as, spike (S), nucleoprotein (N), membrane (M) and envelope (E) proteins also possess APRs in their primary structures which altogether constitute 30% of the total APRs identified. Our findings may provide new windows of opportunities to design specific peptide-based, anti-SARS-CoV-2 therapeutic molecules against COVID-19.

Biofilms have significant role in microbial persistence, antibiotic resistance and chronic infections; consequently, there is a pressing need for development of novel “anti-biofilm strategies”. One of the fundamental mechanisms involved in biofilm formation is protein-protein interactions of ‘amyloid like proteins’ (ALPs) in extracellular matrix. Such interactions could be potential targets for development of novel anti-biofilm strategies; therefore, assessing the structural features of these interactions could be of great scientific value. Characterization of biomolecular interaction with conventional structure biology tools including X-Ray diffraction and Nuclear Magnetic Resonance is technically challenging, expensive and time-consuming. In contrast, modelling such interactions is time-efficient, economical and might provide deeper understanding of structural basis of interactions. Therefore, during the present study, protein-protein interaction of TasA(28-261)–TapA(33-253) (which is a decisive process for biofilm formation by Bacillus subtilis) was modeled using in silico approaches viz., molecular modelling, protein-protein docking and molecular dynamics simulations. Results identified amino-acid residues present within intrinsically disordered regions of both proteins to be critical for interaction. These results were further supported with PCA and FEL analyses. Results presented here represent novel finding and we hypothesize that aa identified during the present study could be targeted for inhibition of biofilm formation by B. subtilis.

Biofilms have a significant role in microbial persistence, antibiotic resistance, and chronic infections; consequently, there is a pressing need for development of novel "anti-biofilm strategies." One of the fundamental mechanisms involved in biofilm formation is protein-protein interactions of "amyloid-like proteins" (ALPs) in the extracellular matrix. Such interactions could be potential targets for development of novel anti-biofilm strategies; therefore, assessing the structural features of these interactions could be of great scientific value. Characterization of structural features the of protein-protein interaction with conventional structure biology tools including X-ray diffraction and nuclear magnetic resonance is technically challenging, expensive, and time-consuming. In contrast, modeling such interactions is time-efficient and economical, and might provide deeper understanding of structural basis of interactions. Although it is often acknowledged that molecular modeling methods have varying accuracy, their careful implementation with supplementary verification methods can provide valuable insight and directions for future studies. With this reasoning, during the present study, the protein-protein interaction of TasA

Amyloid fibrils are linear polypeptide aggregates with a cross-β structure. These fibrils are best known for their association with neurodegenerative diseases, such as Alzheimer's or Parkinson's, but they may also be used by living organisms as functional units, e.g. in the synthesis of melanin or in the formation of bacterial biofilms. About a decade ago, in a search for semen factors that modulate infection by HIV-1 (a sexually transmitted virus and the causative agent of the acquired immune deficiency syndrome (AIDS)), it was demonstrated that semen harbors amyloid fibrils capable of markedly increasing HIV infection rates. This discovery not only created novel opportunities to prevent sexual HIV-1 transmission but also stimulated research to unravel the natural role of these factors. We discuss here the identification of these intriguing structures, their molecular properties, and their effects on both sexually transmitted diseases and reproductive health. Moreover, we review strategies to antagonize semen amyloid to prevent sexual transmission of viruses.

Since the discovery of Acquired Immuno Deficiency Syndrome (AIDS) in 1981 in United States, there have been tremendous efforts to reduce the rate of HIV transmission. Although, the epidemic is stabilized in most of the affected regions, its occurrence is reasonably evident in Eastern Europe and Central Asia due to high rate of new HIV infections. It is surprising to know that despite the high rate of infection, the virus is a weak pathogen. This paradox has been answered by a recent discovery stating that human semen contains a proteinaceous factor derived from prostatic acid phosphatase (PAP), which is commonly known as PAP248-286 peptide, plays an important role in enhancing the HIV infectivity. It forms well-defined amyloid structure, frequently referred as Semen-derived Enhancer of Viral Infection (SEVI) and enhances HIV infection up to 1,00,000 fold. Serendipitous discovery of this semen derived amyloid has provided an opportunity to design an alternative approach to dismantle the mechanism of HIV infection. It is a need of the hour to search and design novel molecules and compounds that can help in destabilizing SEVI under natural conditions. In this direction, a number of molecules have been identified that have shown promising results under laboratory conditions. However, there are several critical issues that remain untouched and their addressal is highly recommended in order to develop an effective regime to control the HIV transmission via sexual route. This review is an effort to consolidate major challenges in developing a therapeutic strategy against semen derived amyloids to combat HIV transmission.

The present study correlates the mechanism of α-amylase denaturation under acidic condition and its structural stabilization in presence of selected cosolvents (sorbitol, sucrose, trehalose, and glycerol). The objective of the present study was to minimize the enzyme inactivation at lower pH by stabilizing the enzyme structure. The above cosolvents were found to be an effective stabilizer of α-amylase against denaturation at extreme low pH. The optimum activity of α-amylase was found to be in the pH range of 4.5 to 7. Decreasing the pH of enzyme solution below this range results in a decrease in enzyme activity. The intrinsic and ANS fluorescence indicated the gradual unfolding of protein below pH 4 and resulted in exposure of hydrophobic cluster. The pH-induced unfolding also resulted in protein aggregation. The intrinsic and 8-anilinonaphathalene-1-sulphonic acid (ANS) fluorescence, acrylamide quenching, near and far UV-CD spectra of α-amylase at lower pH (pH 2.25) indicated the complete loss of tertiar...

Alzheimer's disease (AD) is a fatal neurodegenerative disorder in humans and the main cause of dementia in aging societies. The disease is characterized by the aberrant formation of β-amyloid (Aβ) peptide oligomers and fibrils. These structures may damage the brain and give rise to cerebral amyloid angiopathy, neuronal dysfunction, and cellular toxicity. Although the connection between AD and Aβ fibrillation is extensively documented, much is still unknown about the formation of these Aβ aggregates and their structures at the molecular level. Here, we combined electron cryomicroscopy, 3D reconstruction, and integrative structural modeling methods to determine the molecular architecture of a fibril formed by Aβ(1-42), a particularly pathogenic variant of Aβ peptide. Our model reveals that the individual layers of the Aβ fibril are formed by peptide dimers with face-to-face packing. The two peptides forming the dimer possess identical tilde-shaped conformations and interact with each other by packing of their hydrophobic C-terminal β-strands. The peptide C termini are located close to the main fibril axis, where they produce a hydrophobic core and are surrounded by the structurally more flexible and charged segments of the peptide N termini. The observed molecular architecture is compatible with the general chemical properties of Aβ peptide and provides a structural basis for various biological observations that illuminate the molecular underpinnings of AD. Moreover, the structure provides direct evidence for a steric zipper within a fibril formed by full-length Aβ peptide.

In the present study an attempt was made to investigate the macromolecular crowding effect on functional attributes ofα-amylase. High concentrations of sugar based cosolvents, (e.g., trehalose, sucrose, sorbitol, and glycerol) were used to mimic the macromolecular crowding environment (of cellular milieu) underin vitroconditions. To assess the effect of macromolecular crowding, the activity and structural properties of the enzyme were evaluated in the presence of different concentrations of the above cosolvents. Based on the results it is suggested that the macromolecular crowding significantly improves the catalytic efficiency of the enzyme with marginal change in the structure. Out of four cosolvents examined, trehalose was found to be the most effective in consistently enhancing thermal stability of the enzyme. Moreover, the relative effectiveness of the above cosolvents was found to be dependent on their concentration used.

Naturally occurring fragments of the abundant semen proteins prostatic acid phosphatase (PAP) and semenogelins form amyloid fibrils in vitro. These fibrils boost HIV infection and may play a key role in the spread of the AIDS pandemic. However, the presence of amyloid fibrils in semen remained to be demonstrated. Here, we use state of the art confocal and electron microscopy techniques for direct imaging of amyloid fibrils in human ejaculates. We detect amyloid aggregates in all semen samples and find that they partially consist of PAP fragments, interact with HIV particles and increase viral infectivity. Our results establish semen as a body fluid that naturally contains amyloid fibrils that are exploited by HIV to promote its sexual transmission.

The activity and thermal stability of alpha-amylase were studied in the presence of different concentrations of trehalose, sorbitol, sucrose and glycerol. The optimum temperature of the enzyme was found to be 50 +/- 2 degrees C. Further increase in temperature resulted in irreversible thermal inactivation of the enzyme. In the presence of cosolvents, the rate of thermal inactivation was found to be significantly reduced. The apparent thermal denaturation temperature (Tm) app and activation energy (Ea) of alpha-amylase were found to be significantly increased in the presence of cosolvents in a concentration-dependent manner. In the presence of 40% trehalose, sorbitol, sucrose and glycerol, increments in the (Tm)app were 20 degrees C, 14 degrees C, 13 degrees C and 9 degrees C, respectively. The Ea of thermal denaturation of alpha-amylase in the presence of 20% (w/v) trehalose, sorbitol, sucrose and glycerol was found to be 126, 95, 90 and 43 kcal/mol compared with a control value of 40 kcal/mol. Intrinsic and 8-anilinonaphathalene-1-sulphonic acid (ANS) fluorescence studies indicated that thermal denaturation of the enzyme was accompanied by exposure of the hydrophobic cluster on the protein surface. Preferential interaction parameters indicated extensive hydration of the enzyme in the presence of cosolvents.