Effect of unfolding on the thickness of the hydration layer of a protein

Properties of water in the hydration layer around a protein is intimately correlated with its function. A knowledge of the thickness of the hydration layer is important to understand its role in guiding the folding-unfolding of the protein. We have performed atomistic molecular dynamics simulations of the folded native and a partially unfolded molten globule structure of the villin headpiece subdomain or HP-36 in aqueous solution to estimate the effect of unfolding on the thickness of hydration layer around different segments of the protein. In particular, several dynamic properties of water around different segments of the folded native and the unfolded structure have been calculated by varying the thickness of the hydration layers. It is found that unfolding of a segment of the protein is correlated with the dynamics of water around it, i.e., within the first hydration layer. The effect of unfolding on water properties has been found to diminish when water molecules present beyond the first hydration layer were included in the calculations.      

Brief survey on phytochemicals to prevent COVID-19

BackgroundThe recent pandemic by COVID-19 is a global threat to human health. The disease is caused by SARS-CoV-2 and the infection rate is increased more quickly than MERS and SARS as their rapid adaptation to varied climatic conditions through rapid mutations. It becomes more severe due to the lack of proper therapeutic drugs, insufficient diagnostic tool, scarcity of appropriate drug, life supporting medical facility and mostly lack of awareness. Therefore, preventive measure is one of the important strategies to control. In this context, herbal medicinal plants received a noticeable attention to treat COVID-19 in Indian subcontinent. Here, 44 Indian traditional plants have been discussed with their novel phytochemicals that prevent the novel corona virus. The basic of SARS-CoV-2, their common way of transmission including their effect on immune and nervous system have been discussed. We have analysed their mechanism of action against COVID-19 following in-silico analysis. Their probable mechanism and therapeutic approaches behind the activity of phytochemicals to stimulate immune response as well as inhibition of viral multiplication discussed rationally. Thus, mixtures of active secondary metabolites/phytochemicals are the only choice to prevent the disease in countries where vaccination will take long time due to overcrowded population density.     

Dynamic properties of water around a protein-DNA complex from molecular dynamics simulations

Formation of protein-DNA complex is an important step in regulation of genes in living organisms. One important issue in this problem is the role played by water in mediating the protein-DNA interactions. In this work, we have carried out atomistic molecular dynamics simulations to explore the heterogeneous dynamics of water molecules present in different regions around a complex formed between the DNA binding domain of human TRF1 protein and a telomeric DNA. It is demonstrated that such heterogeneous water motions around the complex are correlated with the relaxation time scales of hydrogen bonds formed by those water molecules with the protein and DNA. The calculations reveal the existence of a fraction of extraordinarily restricted water molecules forming a highly rigid thin layer in between the binding motifs of the protein and DNA. It is further proved that higher rigidity of water layers around the complex originates from more frequent reformations of broken water-water hydrogen bonds. Importantly, it is found that the formation of the complex affects the transverse and longitudinal degrees of freedom of surrounding water molecules in a nonuniform manner.     

Insights into the AIEE of 1,8‐Naphthalimides (NPIs): Inverse Effects of Intermolecular Interactions in Solution and Aggregates

Systematic structural perturbation has been used to fine‐tune and understand the luminescence properties of three new 1,8‐naphthalimides (NPIs) in solution and aggregates. The NPIs show blue emission in the solution state and their fluorescence quantum yields are dependent upon their molecular rigidity. In concentrated solutions of the NPIs, intermolecular interactions were found to quench the fluorescence due to the formation of excimers. In contrast, upon aggregation (in THF / H₂O mixtures), the NPIs show aggregation‐induced emission enhancement (AIEE). The NPIs also show moderately high solid‐state emission quantum yields (ca. 10–12.7 %). The AIEE behaviour of the NPIs depends on their molecular rigidity and the nature of their intermolecular interactions. The NPIs 1 – 3 show different extents of intermolecular (π–π and C?H???O) interactions in their solid‐state crystal structures depending on their substituents. Detailed photophysical, computational and structural investigations suggest that an optimal balance of structural flexibility and intermolecular communication is necessary for achieving AIEE characteristics in these NPIs.     

Cover Picture

The cover picture shows how thrombosis occurs in the deep veins of the lower limbs. Stasis, which results from slow and turbulent blood flow, combined with hypercoagulation, caused, for example, by a surgical procedure, may result in thrombus formation. The synthetic sulfated pentasaccharide shown in part is a potent antithrombotic compound that exerts its effect by activation of the plasma protein antithrombin III. Conformationally locked monosaccharides have now been synthesized to demonstrate that L-iduronic acid, one part of the pentasaccharide, must adopt an unusual distorted conformation to activate antithrombin III. Such conformational effects might be relevant in explaining the unique biological properties of glycosaminoglycans that contain L-iduronic acid. In the background of the picture, a flight of vampire bats is attracted by the pentasaccharide. Vampire was the name given to South American blood-sucking bats (Latin name: desmodus rotundus) in 1761 by the French naturalist Georges Louis Leclerc Comte de Buffon (1707-1788). These bats are known to attack cattle and, very rarely, sleeping human beings. Although their saliva has been shown to contain an anticoagulant compound, they would also be happy to benefit from the pentasaccharide mentioned above, to suck the blood out of the vein more easily. More details about this compound which would be helpful to vampire bats are reported by Petitou, Sina? et al. on p. 1670 ff.     

Modeling and analysis of quadruple optical ring resonator performance as optical filter using Vernier principle

Vernier principle based modeling and analysis of an optical ring resonator structure that includes four asymmetric rings are introduced in this paper to obtain very wide free spectral range (FSR). Delay line signal processing approach in Z-domain modeling is used for analysis of waveguide based novel quadruple optical ring resonator (QORR). Two QORR architectures made of SOI and SiN waveguides have been compared, which produce FSR of 343.4 THz 264.6 THz respectively. Apart from obtaining wider FSR and adequate suppression of spurious interstitial modes close to -30 dB, this work presents group delay and dispersion characteristics for QORR made of materials with different effective refractive indices.     

An Analogue of Bochner’s Theorem for Damek-Ricci Spaces

We characterize the image of radial positive measures θ’s on a harmonic NA group S which satisfies ∫ _S ? ₀(x)?dθ(x)<∞ under the spherical transform, where ? ₀ is the elementary spherical function.     

Wiener–Tauberian type theorems for radial sections of homogenous vector bundles on certain rank one Riemannian symmetric spaces of noncompact type

We will show that an uniform treatment yields Wiener–Tauberian type results for various Banach algebras and modules consisting of radial sections of some homogenous vector bundles on rank one Riemannian symmetric spaces G/K of noncompact type. One example of such a vector bundle is the spinor bundle. The algebras and modules we consider are natural generalizations of the commutative Banach algebra of integrable radial functions on G/K. The first set of them are Beurling algebras with analytic weights, while the second set arises due to Kunze–Stein phenomenon for noncompact semisimple Lie groups.