Molecular properties of Ca2+ transport through TRPV2 channel: a molecular dynamics simulations study.

TRPV channels are a category of nonselective cation channels that are activated by heat and ligands and permeate monovalent and divalent ions. The mechanism of Ca2+ transfer through TRPV2 channel is not well known. Here, we investigated the reaction coordination and energy fluctuation of Ca2+ transition in TRPV2 channel by steered molecular dynamics (SMD) simulations and potential of mean force (PMF) calculation. Results showed that electrostatic interactions between Ca2+ and residues of the first and second gates had main roles in ions transfer through the channel. Also, we recognized important amino acids in this path. Moreover, results indicated that enter and exit of calcium ions need to overcome barrier energies in the first and second gates.Communicated by Ramaswamy H. Sarma.

Role of the Probe Sequence/Structure in Developing an Ultra-Efficient Label-Free COVID-19 Detection Method Based on Competitive Dual-Emission Ratiometric DNA-Templated Silver Nanoclusters as Single Fluorescent Probes.

We report the development of a label-, antibody-, enzyme-, and amplification-free ratiometric fluorescent biosensor for low-cost and rapid (less than 12 min) diagnosis of COVID-19 from isolated RNA samples. The biosensor is designed on the basis of cytosine-modified antisense oligonucleotides specific for either N gene or RdRP gene that can form silver nanoclusters (AgNCs) with both green and red emission on an oligonucleotide via a one-step synthesis process. The presence of the target RNA sequence of SARS-CoV-2 causes a dual-emission ratiometric signal transduction, resulting in a limit of detection of 0.30 to 10.0 nM and appropriate linear ranges with no need for any further amplification, fluorophore, or design with a special DNA fragment. With this strategy, five different ratiometric fluorescent probes are designed, and how the T/C ratio, the length of the stem region, and the number of cytosines in the loop structure and at the 3' end of the cluster-stabilizing template can affect the biosensor sensitivity is investigated. Furthermore, the effect of graphene oxide (GO) on the ratiometric behavior of nanoclusters is demonstrated and the concentration-/time-dependent new competitive mechanism between aggregation-caused quenching (ACQ) and aggregation-induced emission enhancement (AIE) for the developed ssDNA-AgNCs/GO nanohybrids is proposed. Finally, the performance of the designed ratiometric biosensor has been validated using the RNA extract obtained from more than 150 clinical samples, and the results have been confirmed by the FDA-approved reverse transcription-polymerase chain reaction (RT-PCR) diagnostic method. The diagnostic sensitivity and specificity of the best probe is more than >90%, with an area under the receiver operating characteristic (ROC) curve of 0.978.

Structural Analysis and Conformational Dynamics of Short Helical Hyperphosphorylated Segments of Tau Protein (Sequence 254-290) in Alzheimer's Disease: A Molecular Dynamics Simulation Study.

Alzheimer's disease (AD) is a progressive neurodegenerative disorder whose early diagnosis leads to a chance for successful treatment and decreases the side effects. Hyperphosphorylation of tau proteins is a pathological hallmark of AD that causes it to lose its attachment ability to the microtubules. Alteration of tau structure due to its hyperphosphorylation is an exciting challenge regarding AD treatments. Here, we aimed to examine the structural alterations of short helical segments of tau protein with one to three phosphorylated sites by molecular dynamics simulation. Results indicated that the interaction of two similar segments with three phosphorylated sites (P-Ser262, 285, and 289) formed a compact and more stable structure than the one phosphorylated site complex (P-Ser262). Moreover, due to the high dynamics of the P-Ser262 complex, several structures were made with different conformational dynamics, but there was only one stable cluster of the P-Ser262, 285, and 289 complex during simulation. It seems that the P-Ser262, 285, and 289 complex plays an important role in the formation of paired helical filaments (PHFs) by forming a stable dimer. Generally, it is important to identify how structural features of segments in tau protein change when the phosphorylated sites increase from one to three sites and their effects on the formation of PHFs for drug design and diagnostic biomarkers.

Static and Electromagnetic Fields Differently Affect Proliferation and Cell Death Through Acid Enhancement of ROS Generation in Mesenchymal Stem Cells.

Magnetic fields remotely influence cellular homeostasis as a physical agent through the changes in cell physicochemical reactions. Magnetic fields affect cell fate, which may provide an important and interesting challenge in stem cell behaviors. Here, we investigated the effects of the static magnetic field (SMF, 20 mT) and electromagnetic field (EMF, 20 mT-50 Hz) on reactive oxygen species (ROS) production and the acidic pH conditions as stimuli to change cell cycle progression and cell death in mesenchymal stem cells. Results show that SMF, EMF, and their simultaneous (SMF+EMF) administration increase ROS and expression of nuclear factor erythroid 2-related factor 2 (Nrf2), superoxide dismutase 2 (SOD2), and glutathione-S-transferase (GST) as an antioxidant defense system. Besides, intracellular pH (pHi) decreases in presence of either EMF or SMF+EMF, but not SMF. Decreased ROS content using ascorbic acid in these treatments leads to increased pH compared to the magnetic field treatments alone. Furthermore, each magnetic field has different effects on the cellular process of stem cells, including cell cycle, apoptosis and necrosis. Moreover, treatment by SMF enhances the cell viability after 24 h, while EMF or SMF+EMF decreases it. These observations indicate that fluctuations of ROS generation and acid enhancement during SMF and EMF treatments may reveal their beneficial and adverse effects on the molecular and cellular mechanisms involved in the growth, death, and differentiation of stem cells.

Taxoid profile in endophytic fungi isolated from Corylus avellana, introduces potential source for the production of Taxol in semi-synthetic approaches.

Taxol (Paclitaxel) and its derivative taxanes are widely used in chemotherapy and treatment of different types of cancer. Although the extracted taxanes from Taxus sp. are currently used in semi-synthetic production of Taxol, providing alternative always available sources is still a main concern. Due to availability and fast growth rate, microorganisms are much potent alternative sources for taxanes. In the present study, 249 endophytic fungi were isolated from Corylus avellana at six different locations of Iran, among which 18 species were capable to produce taxanes. Genotyping analysis indicated that 17 genera were ascomycetes but only one basidiomycete. Seven taxanes were detected and quantified in solid and suspension cultures by HPLC and their structures were confirmed by LC-Mass analysis. Among endophytes, CA7 had all 7 taxoids and CA1 had the highest Taxol yield. In 78% of endophytes transferring to liquid media was accompanied by increase of taxanes yield and increased taxan production and its release to media up to 90%. Evaluation of cytotoxicity indicated that extracts of all isolated fungi were lethal to MCF7 cells. Since endophytes produced remarkable amounts of taxanes, they can be suggested as alternative inexpensive and easily available resources for Taxol production in semi-synthesis plans.

Inhibition potential evaluation of two synthetic bis-indole compounds on amyloid fibrillation: a molecular simulation study.

Protein aggregation is known as the main mechanism of amyloid fibrillation in amyloidosis diseases. Recent studies confirmed that compounds with one or two indole rings have inhibitory potential against amyloid fibrillation. Herein, the interaction of two similar compounds 'bis(indolyl)-2-methyl-phenyl-methene' and 'bis(indolyl)-2-chloro-phenyl-methene' with an amyloid core model was investigated. To this aim, molecular docking and all-atom molecular dynamics (MD) simulations were used. Docking results between aggregation-prone region (APR) of hen egg-white lysozyme (HEWL) and either of ligands showed that they interact with different residues of the APR (amyloid fibril nucleus). According to MD results, bis(indolyl)-2-methyl-phenyl-methene made a distance between the two cores, which was 1.5 times greater than that bis(indolyl)-2-chloro-phenyl-methene made. Analysis of RMSD/RMSF values revealed that bis(indolyl)-2-methyl-phenyl-methene stabilized strands of A and B, while destabilized strands C and D. The hydrophobic 'methyl' functional group in bis(indolyl)-2-methyl-phenyl-methene facilitate its deep penetration between core nuclei, via destabilizing outer strands of C and D. Considering this fact that results of this study are in agreement with experimental findings, details of the discovered mechanism of interaction between ligands and HEWL's APR would be inspiring for further anti-fibrillation drug designs.Communicated by Ramaswamy H. Sarma.

Fluorescent Nanoclusters for Imaging of Cells/Stem Cells.

Imaging of cancer cells and cancer stem cells (CSCs) plays an important role in studying cell biology and tracking cancer development and metastasis. There is a wide interest in targeting cancer cells using fluorescent nanoclusters (NCs) capped in protein due to excellent cell viability and photostability, one-step synthesis route, large Stokes shift, good aqueous stability, and easy functionalization capability with long lifetime. Since CD44 is a CSC marker as well as a transmembrane receptor for hyaluronic acid (HA) and many other extracellular matrix (ECM) components, in this protocol, a biocompatible platform was synthesized by conjugation of HA onto luminescent platinum nanoclusters (Pt NCs) in human hemoglobin (Hb) (Hb/Pt NCs). This bioplatform could be used for specific imaging via an efficient targeting of CD44-overexpressing cancer cells and cancer stem cells.