Biotechnological storage and utilization of entrapped solar energy

Our laboratory has recently developed a device employing immobilized F₀F₁ adenosine triphosphatase (ATPase) that allows synthesis of adenosine triphosphate (ATP) from adenosine 5′-diphosphate and inorganic phosphate using solar energy. We present estimates of total solar energy received by Earth’s land area and demonstrate that its efficient capture may allow conversion of solar energy and storage into bonds of biochemicals using devices harboring either immobilized ATPase or NADH dehydrogenase. Capture and storage of solar energy into biochemicals may also enable fixation of CO₂ emanating from polluting units. The cofactors ATP and NADH synthesized using solar energy could be used for regeneration of acceptor d-ribulose-1,5-bisphosphate from 3-phosphoglycerate formed during CO₂ fixation.     

Sensitivity of polar solvation dynamics to the secondary structures of aqueous proteins and the role of surface exposure of the probe

The structure and dynamics of water around a protein is expected to be sensitive to the details of the adjacent secondary structure of the protein. In this article, we explore this sensitivity by calculating both the orientational dynamics of the surface water molecules and the equilibrium solvation time correlation function of the polar amino acid residues in each of the three helical segments of the protein HP-36, using atomistic molecular dynamics simulations. The solvation dynamics of polar amino acid residues in helix-2 is found to be faster than that of the other two helices (the average time constant is smaller by a factor of 2), although the interfacial water molecules around helix-2 exhibit much slower orientational dynamics than that around the other two helices. A careful analysis shows that the origin of such a counterintuitive behavior lies in the dependence of the solvation time correlation function on the surface exposure of the probe-the more exposed is the probe, the faster the solvation dynamics. We discuss that these results are useful in explaining recent solvation dynamics experiments.     

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.     

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.     

Fine‐Tuning Dual Emission and Aggregation‐Induced Emission Switching in NPI–BODIPY Dyads

Three new NPI–BODIPY dyads 1 – 3 (NPI=1,8‐naphthalimide, BODIPY=boron‐dipyrromethene) were synthesized, characterized, and studied. The NPI and BODIPY moieties in these dyads are electronically separated by oxoaryl bridges, and the compounds only differ structurally with respect to methyl substituents on the BODIPY fluorophore. The NPI and BODIPY moieties retain their optical features in molecular dyads 1 – 3 . Dyads 1–3 show dual emission in solution originating from the two separate fluorescent units. The variations of the dual emission in these compounds are controlled by the structural flexibilities of the systems. Dyads 1 – 3 , depending on their molecular flexibilities, show considerably different spectral shapes and dissimilar intensity ratios of the two emission bands. The dyads also show significant aggregation‐induced emission switching (AIES) on formation of nano‐aggregates in THF/H₂O with changes in emission color from green to red. Whereas the flexible and aggregation‐prone compound 1 shows AIES, rigid systems with less favorable intermolecular interactions (i.e., 2 and 3 ) show aggregation‐induced quenching of emission. Correlations of the emission intensity and structural flexibility were found to be reversed in solution and aggregated states. Photophysical and structural investigations suggested that intermolecular interactions (e.g., π–π stacking) play a major role in controlling the emission of these compounds in the aggregated state.     

Information and Entropy Flow in the Kalman–Bucy Filter

We investigate the information theoretic properties of Kalman–Bucy filters in continuous time, developing notions of information supply, storage and dissipation. Introducing a concept of energy, we develop a physical analogy in which the unobserved signal describes a statistical mechanical system interacting with a heat bath. The abstract universe comprising the signal and the heat bath obeys a non-increase law of entropy; however, with the introduction of partial observations, this law can be violated. The Kalman–Bucy filter behaves like a Maxwellian demon in this analogy, returning signal energy to the heat bath without causing entropy increase. This is made possible by the steady supply of new information. In a second analogy the signal and filter interact, setting up a stationary non-equilibrium state, in which energy flows between the heat bath, the signal and the filter without causing any overall entropy increase. We introduce a rate of interactive entropy flow that isolates the statistical mechanics of this flow from marginal effects. Both analogies provide quantitative examples of Landauers Principle.     

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.     

Conformational fluctuations of a protein-DNA complex and the structure and ordering of water around it

Protein-DNA binding is an important process responsible for the regulation of genetic activities in living organisms. The most crucial issue in this problem is how the protein recognizes the DNA and identifies its target base sequences. Water molecules present around the protein and DNA are also expected to play an important role in mediating the recognition process and controlling the structure of the complex. We have performed atomistic molecular dynamics simulations of an aqueous solution of the protein-DNA complex formed between the DNA binding domain of human TRF1 protein and a telomeric DNA. The conformational fluctuations of the protein and DNA and the microscopic structure and ordering of water around them in the complex have been explored. In agreement with experimental studies, the calculations reveal conformational immobilization of the terminal segments of the protein on complexation. Importantly, it is discovered that both structural adaptations of the protein and DNA, and the subsequent correlation between them to bind, contribute to the net entropy loss associated with the complex formation. Further, it is found that water molecules around the DNA are more structured with significantly higher density and ordering than that around the protein in the complex.     

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.