Structural insight to human Retinoid X receptor alpha-Thyroid hormone receptor beta heterodimer by molecular modelling and MD-simulation studies: role of conserved water molecules.

The Retinoid X receptor alpha-Thyroid hormone receptor beta (RXRα-THRß) heterodimer plays an important role in physiological function of humans specially in the growth and development. Extensive MD-simulation studies on the aquated complexes of modelled RXRα-THRß heterodimer with DNA-duplex have indicated the role of some conserved/semiconserved water molecules in the complexation process in presence or absence of Triiodothyronine (T3) and 9-cis retinoic acid (9CR) in the respective Ligand Binding Domain (LBD) domain. Among the seventeen conserved/semi-conserved water molecules, the W1-W4 water centers have been observed to mediate the interaction between the residues of A-chain (DBD of RXR) to consensus sequence (C-chain) of DNA. The W5-W8 water centers involve in recognition of the residues of B-chain (DBD of THR) to C-chain of DNA. The W9-W13 centers have connected the different residues of B-chain (THR) to D-chain of DNA through H-bonds, whereas W14-W17 water molecules were involved in the interaction of A-chain's (RXR) residues to D-chain of DNA. In our previous study with homodimeric THRß from Rattus norvegicus we have identified fifteen conserved water molecules at the DNA-DBD interface. Moreover, the conformational flexibility of Met313 (in the LBD of THR) from open to close form in presence or absence of T3 molecule in the holo and Apo-protein may provide a plausible rational on the possible role of that residue to acts as gate which could restrict the solvent molecules to enter into the hydrophobic T3-binding pocket of LBD during the absence of ligand molecule and thus could help the stabilization of that domain in THRß structure.Communicated by Ramaswamy H. Sarma.

A rhodamine-based dual chemosensor for Cu(II) and Fe(III).

An "off-on" rhodamine-based fluorescence probe for the selective signaling of Cu(II) and Fe(III) has been designed and synthesized. The optical properties of this compound have been investigated in acetonitrile-water (1:1) binary solution. Very interestingly, this compound showed sensitivity and selectivity towards Cu(II) during absorption process and towards Fe(III) during emission process. So this is a nice example of an excellent dual chemosensor for two biologically/physiologically very important transition metal ions using only the two very different techniques (absorption and emission); both cases displayed only intensity enhancement.

Self-Assembly of Solvent-Stabilized Au Nanocluster as Efficient Förster Resonance Energy-Transfer Initiator for White Light Generation.

Aggregation-induced enhancement (AIE) in the photoluminescence quantum yield (PLQY) from 12.5 to 51% in the N,N-dimethylformamide (DMF)-stabilized Au nanocluster (AuNC) system is reported here. The self-assembling of AuNC has been achieved via hydrogen bonding interaction, which is further utilized in designing the AuNC_DCM system for realizing a Förster resonance energy transfer (FRET)-based white LED (WLED), having CIE coordinates of (0.35, 0.29). The solution-processed fabrication strategy used, has given us the liberty to optimize its components for optimal full-spectrum light output. The CIE coordinates of the designed WLED have been improved further to (0.33, 0.32), with a high color rendering index of 93 and correlated color temperature of 5620 K by incorporating a green emitter, namely nitrogen-doped graphene quantum dots (NGQD), in the AuNC_DCM system. The excellent spectral quality of the as-designed WLED and the repeatability of the proposed fabrication method will make the developed AuNCs_DCM FRET conjugate useful in practical photonic applications.

Structural insight to hydroxychloroquine-3C-like proteinase complexation from SARS-CoV-2: inhibitor modelling study through molecular docking and MD-simulation study.

The spread of novel coronavirus strain, Severe Acute Respiratory Syndrome 2 (SARS-CoV-2) causes Coronavirus disease (COVID-19) has now spread worldwide and effecting the entire human race. The viral genetic material is transcripted and replicated by 3 C-like protease, as a result, it is an important drug target for COVID-19. Hydroxychloroquine (HCQ) report promising results against this drug target so, we perform molecular docking followed by MD-simulation studies of HCQ and modelled some ligand (Mod-I and Mod-II) molecules with SARS-CoV-2-main protease which reveals the structural organization of the active site residues and presence of a conserve water-mediated catalytic triad that helps in the recognition of Mod-I/II ligand molecules. The study may be helpful to gain a detailed structural insight on the presence of water-mediated catalytic triad which could be useful for inhibitor modelling. Communicated by Ramaswamy H. Sarma.

Molecular modeling and molecular dynamics simulation studies on thyroid hormone receptor from Rattus norvegicus: role of conserved water molecules.

Thyroid hormone receptor (THR) belongs to the nuclear receptor (NR) superfamily that is activated by binding of appropriate ligand molecules (thyroid hormones). These receptors directly bind to specific DNA sequences for gene expression, which is essential for metabolism, homeostasis, and the development of organisms, making it an important drug target. Extensive MD-simulation studies of triiodothyronine (T3) docked modeled rnTHRß1 structures have indicated the presence of twelve conserved water molecules at the DNA-DBD (DNA binding domain) interface. The W1-W5 water centers have been involved in the recognition between the A-chain of DBD to C-chain of DNA, W6 and W7 mediated the interaction between A-chain of DBD and D-chain of DNA, W8 and W9 recognized the B-chain of DBD and C-chain of DNA, and W9-W12 centers conjugated the residues of B-chain of DBD to D-chain of DNA through hydrogen bonds. The conformation flexibility of Phe272 and Met313 residues in the absence of T3 at the LBD (ligand-binding domain) region have been observed and reported.

Absorption-Dominated Electromagnetic Wave Suppressor Derived from Ferrite-Doped Cross-Linked Graphene Framework and Conducting Carbon.

To minimize electromagnetic (EM) pollution, two key parameters, namely, intrinsic wave impedance matching and intense absorption of incoming EM radiation, must satisfy the utmost requirements. To target these requirements, soft conducting composites consisting of binary blends of polycarbonate (PC) and poly(vinylidene fluoride) (PVDF) were designed with doped multiwalled carbon nanotubes (MWCNTs) and a three-dimensional cross-linked graphene oxide (GO) framework doped with ferrite nanoparticles. The doping of α-MnO2 onto the MWCNTs ensured intrinsic wave impedance matching in addition to providing conducting pathways, and the ferrite-doped cross-linked GO facilitated the enhanced attenuation of the incoming EM radiation. This unique combination of magnetodielectric coupling led to a very high electromagnetic shielding efficiency (SE) of -37 dB at 18 GHz, dominated by absorption-driven shielding. The promising results from the composites further motivated us to rationally stack individual composites into a multilayer architecture following an absorption-multiple reflection-absorption pathway. This resulted in an impressive SE of -57 dB for a thin shield of 0.9-mm thickness. Such a high SE indicates >99.999% attenuation of the incoming EM radiation, which, together with the improvement in structural properties, validates the potential of these materials in terms of applications in cost-effective and tunable solutions.