Computational Investigation into the Interactions of Traditional Chinese Medicine Molecules of WenQingYin with GluR2.

Docking and molecular dynamics simulations have been carried out to investigate the interaction of a traditional Chinese medicine, WenQingYin, with the glutamate receptor 2 (GluR2) subunit of the α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor. Four representative drug components of WenQingYin, namely 2-(3,4-dihydroxyphenyl)-5,6,7-trihydroxy-4H-chromen-4-one (PHF), 4-hydroxy-3-methoxybenzoic acid (HMB), 4-(2,3-dihydroxy-3-methylbutoxy)-7H-furo[3,2-g]chromen-7-one (DHMBP) and methyl 7-formylcyclopenta[c]pyran-4-carboxylate (cerbinal), and their complexes with GluR2 were simulated. Our results show that PHF, HMB, and DHMBP formed a partial hydrogen bond with GluR2 in its ligand-binding domain. However, cerbinal was not stable in the ligand-binding domain of GluR2 and induced a significant change in the structure of GluR2. Three-dimensional plots represent the contact and movement situation of the traditional Chinese medicine molecules in the ligand-binding domain. The combined results of the docking and molecular dynamics simulations provide insight into the interaction between these traditional Chinese medicine molecules and proteins.

Transient knockdown-mediated deficiency in plectin alters hepatocellular motility in association with activated FAK and Rac1-GTPase.

BACKGROUND: Plectin is one of the cytolinker proteins that play a crucial role in maintaining the integrity of cellular architecture. It is a component of desmosome complexes connecting cytoskeletal proteins and trans-membrane molecules. In epithelial cells, plectin connects cytokeratins and integrin α6ß4 in hemidesmosomes anchoring to the extracellular matrix. In addition to the function of molecular adherent, plectin has been reported to exhibit functions affecting cellular signals and responsive activities mediated by stress, cellular migration, polarization as well as the dynamic movement of actin filaments. Plectin deficiency in hepatocellular carcinoma results in abnormal expression of cytokeratin 18 and disassembled hemidesmosome. Therefore, it is hypothesized that the plectin deficiency-mediated collapse of cytoskeleton may modulate cellular motility that is associated with consequent metastatic behaviors of cancer cells. METHODS AND RESULTS: The cellular motility of plectin-deficient Chang liver cells generated by transient knockdown were analyzed by trans-well migration assay and the results revealed a higher migration rate. The confocal microscopy also demonstrated less organized and more polarized morphology as well as more focal adhesion kinase activity in comparison with that of the mock Chang liver cells. Furthermore, plectin-knockdown in Chang liver cells was associated with a higher activity of Rac1-GTPase in accordance with the results of the Rac1 pull-down assay. The immunohistochemical assay on human hepatocellular carcinoma showed that the expression of focal adhesion kinase was increased in the invasive front of tumor. CONCLUSION: Plectin-deficient human hepatic cells exhibit higher cell motility associated with increase in focal adhesion kinase activity that are comparable to the properties of invasive hepatocellular carcinoma.

Effect of Side Chain Length on Polycarboxylate Superplasticizer in Aqueous Solution: A Computational Study.

Molecular dynamics simulations were carried out to study the conformations of polycarboxylate ether (PCE) superplasticizers with different side chain lengths in aqueous solution. For four types of PCE molecules-PCE1, PCE2, PCE3, and PCE4-the steric hindrance between the PCE molecules increased with increasing side chain length. The side chain length not only affects water mobility but also affects the distribution of water molecules in the system. Simulation results indicate that water molecules were trapped by the PCE molecules, reducing the diffusion properties. PCE molecules with long side chains have more water molecules probability around the main chain and fewer water molecules probability near the side chain. Microscopic-level knowledge of the interaction between superplasticizer and water molecules facilitates understanding of the performance of superplasticizers in cement systems.

Graphene Wrinkles affect electronic transport in nanocomposites: Insight from molecular dynamics simulations.

Molecular dynamics (MD) simulations were carried out to study the physical properties of graphene-oxide (GO) and polydimethylsiloxane (PDMS) interfacial systems. Simulations were performed for GO molecules dispersed into short-chain, long-chain, and long-chain and cross-linked PDMS polymers. Various structural properties, dipole moments and dielectric constants of the graphene-oxide molecules were calculated, which were correlated with the electron transport properties of the GO/PDMS system. The effects of polymer length and type of linkage on transport properties were also examined.

Plectin deficiency in liver cancer cells promotes cell migration and sensitivity to sorafenib treatment.

Plectin involved in activation of kinases in cell signaling pathway and plays important role in cell morphology and migration. Plectin knockdown promotes cell migration by activating focal adhesion kinase and Rac1-GTPase activity in liver cells. Sorafenib is a multi-targeting tyrosine kinase inhibitor that improves patient survival on hepatocellular carcinoma. The aim of this study is to investigate the correlation between the expression of plectin and cell migration as well as the sensitivity of hepatoma cell lines exposing to sorafenib. Hepatoma cell lines PLC/PRF/5 and HepG2 were used to examine the level of plectin expression and cell migration in comparison with Chang liver cell line. In addition, sensitivity of the 3 cell lines to sorafenib treatment was also measured. Expression of plectin was lower in PLC/PRF/5 and HepG2 hepatoma cells than that of Chang liver cells whereas HepG2 and PLC/PRF/5 cells exhibit higher rate of cell migration in trans-well migration assay. Immunohistofluorecent staining on E-cadherin revealed the highest rate of collective cell migration in HepG2 cells and the lowest was found in Chang liver cells. Likewise, HepG2 cell line was most sensitive to sorafenib treatment and Chang liver cells exhibited the least sensitivity. The drug sensitivity to sorafenib treatment showed inverse correlation with the expression of plectin. We suggest that plectin deficiency and increased E-cadherin in hepatoma cells were associated with higher rates of cell motility, collective cell migration as well as higher drug sensitivity to sorafenib treatment.

Cell Pleomorphism and Cytoskeleton Disorganization in Human Liver Cancer.

BACKGROUND/AIM: Nucleoskeleton maintains the framework of a cell nucleus that is required for a variety of nuclear functions. However, the nature of nucleoskeleton structure has not been yet clearly elucidated due to microscopy visualization limitations. Plectin, a nuclear pore-permeable component of cytoskeleton, exhibits a role of cross-linking between cytoplasmic intermediate filaments and nuclear lamins. Presumably, plectin is also a part of nucleoskeleton. Previously, we demonstrated that pleomorphism of hepatoma cells is the consequence of cytoskeletal changes mediated by plectin deficiency. In this study, we applied a variety of technologies to detect the cytoskeletons in liver cells. MATERIALS AND METHODS AND RESULTS: The images of confocal microscopy did not show the existence of plectin, intermediate filaments, microfilaments and microtubules in hepatic nuclei. However, in the isolated nuclear preparation, immunohistochemical staining revealed positive results for plectin and cytoskeletal proteins that may contribute to the contamination derived from cytoplasmic residues. Therefore, confocal microscopy provides a simple and effective technology to observe the framework of nucleoskeleton. Accordingly, we verified that cytoskeletons are not found in hepatic cell nuclei. Furthermore, the siRNA-mediated knockdown of plectin in liver cells leads to collapsed cytoskeleton, cell transformation and pleomorphic nuclei. CONCLUSION: Plectin and cytoskeletons were not detected in the nuclei of liver cells compared to the results of confocal microscopy. Despite the absence of nuclear plectin and cytoskeletal filaments, the evidence provided support that nuclear pleomorphism of cancer cells is correlated with the cytoplasmic disorganization of cytoskeleton.

Estimation of electron transfer properties of ferrocenyl-dicholesteryl-peptide in liquid and gel.

Molecular dynamics simulations were carried out to investigate the conformations of ferrocenyl-dicholesteryl N-formamidoformamide (Fc-LS2) molecules in solvents of methanol and 1-propanol. Fc-LS2 comprises ferrocene and cholesteryl units linked by a biocompatible N-formamidoformamide peptide unit. Our results showed that Fc-LS2 formed a gel with 1-propanol but not with methanol. Charge-transfer properties of Fc-LS2/1-propanol gel and Fc-LS2/methanol liquid were also investigated by quantum mechanical (QM) calculations. The QM results indicate that the amino acid linkages contribute to improved charge-transport properties and the transfer integrals of Fc-LS2/1-propanol are larger than those of Fc-LS2/methanol.