Theoretical Study on Zigzag Boron Nitride Nanowires.

In this work, two kinds of BN-nanowires (BNnws): a-BNnw and d-BNnw, respectively composed of azo (N-N) and diboron (B-B) bonds, are proposed with the aid of the first-principles simulations. Their structural stabilities are carefully verified from the energetics, lattice dynamics, and thermodynamic perspectives. Similar to the other common boron nitride polymorph, the a-BNnw and d-BNnw are semiconductors with relatively wide band gaps of 3.

[Speciation and Risk Characteristics of Heavy Metals in the Sediments of the Yangtze Estuary].

Based on the investigation on the distribution of total contents and speciation of 8 heavy metals (As, Cd, Cr, Cu, Hg, Ni, Pb, Zn) in the surface sediments at 14 typical sites of the Yangtze Estuary during three hydrological seasons ( wet, normal, and dry seasons) , this study applied equilibrium partitioning approach to build the sediment quality guidelines (SQGs) of the Yangtze Estuary, and assessed ecological risks of the heavy metals. The relationship between ecological risk and speciation of heavy metals was also revealed. The results showed that, except for Cd, the residual fraction was the main speciation of heavy metals, especially for As, Cr and Hg, their residual fraction proportions were all over 90%.

Investigation on critical structural motifs of ligands for triggering glucocorticoid receptor nuclear migration through molecular docking simulations.

The glucocorticoid receptor (GR), a transcription factor regulating gene expression in a ligand-dependent fashion, is known for flexibility in adapting various ligands with their structures ranging from steroid to non-steroid. However, in our previous study, GR shows a stringent discrimination against a set of steroid ligands with highly similar structures for triggering its nuclear migration. In order to resolve this puzzle, we employed molecular docking simulations to investigate the origin of this structural discrimination.

Enhancing the potency of lithospermate B for inhibiting Na+/K+-ATPase activity by forming transition metal ion complexes.

Aim: To determine whether replacing Mg(2+) in magnesium lithospermate B (Mg-LSB) isolated from danshen (Salvia miltiorrhiza) with other metal ions could affect its potency in inhibition of Na(+)/K(+)-ATPase activity.

Methods: Eight metal ions (Na(+), K(+), Mg(2+), Cr(3+), Mn(2+), Co(2+), Ni(2+), and Zn(2+)) were used to form complexes with LSB. The activity of Na(+)/K(+)-ATPase was determined by measuring the amount of inorganic phosphate (Pi) liberated from ATP.

High-level expression, purification and production of the fungal immunomodulatory protein-gts in baculovirus-infected insect larva.

Fip-gts, a fungal immunomodulatory protein (Fip) isolated from Ganoderma tsugae (gts), has been reported to possess therapeutic effects in the treatment of cancer and autoimmune disease. To cost-effectively produce Fip-gts and bypass the bottleneck involved in its time-consuming purification from G. tsugae, in this study, we incorporated the SP(bbx) secretion signal into recombinant baculovirus for expressing glycosylated and bioactive rFip-gts in baculovirus-infected insect cells and Trichoplusia ni larva.

Site specificity on OH α-H abstraction reaction for a zwitterionic β-hairpin peptide in aqueous solution: a theoretical investigation.

Protein backbone oxidation was investigated by studying the α-H abstraction reaction in a ß-hairpin peptide, called Chignolin (PDB ID 1UAO), with density functional theory calculation at B3LYP/6-31G(d,p) without any constraint. In order to stabilize the zwitterionic form of Chignolin with the salt bridges, the effects of aqueous solution were implemented by using microsolvation combined with a conductor-like polarizable continuum model (CPCM). Comparison between three glycine residues located at three different sites in Chignolin was used to examine the possible site specificity of this backbone oxidation.

Solution structure of a phytocystatin from Ananas comosus and its molecular interaction with papain.

The structure of a recombinant pineapple cystatin (AcCYS) was determined by NMR with the RMSD of backbone and heavy atoms of twenty lowest energy structures of 0.56 and 1.11 Å, respectively.

Inhibition of Na(+)/K(+) -ATPase by antcins, unique steroid-like compounds in Antrodia camphorate.

The inhibition of Na(+)/K(+) -ATPase by versatile steroid-like compounds contributes to the putative therapeutic effects of many Chinese medicinal cardiac products via the same molecular mechanism triggered by cardiac glycosides. Five major steroid-like compounds, antcin A, B, C, H, and K were isolated from Niuchangchih (Antrodia camphorata), a unique Taiwan mushroom, and all inhibited Na(+)/K(+) -ATPase. Antcin A exhibited significantly higher inhibitory potency than the other four antcins, though weaker than ginsenoside Rh2 .

Binding orientation and specificity of calmodulin to rat olfactory cyclic nucleotide-gated ion channel.

Calmodulin (CaM), the primary intracellular Ca(2+) receptor, regulates a large number of key enzymes and controls a wide spectrum of important biological responses. Recognition between CaM and its target sequence in rat olfactory cyclic nucleotide-gated ion channel (OLFp) was investigated by circular dichroism (CD), fluorescence, and NMR spectroscopy. Fluorescence data showed the OLFp tightly bound to CaM with a dissociation constant of 12 nM in a 1:1 stoichiometry.

Oxygen radical-mediated oxidation reactions of an alanine peptide motif - density functional theory and transition state theory study.

Background: Oxygen-base (O-base) oxidation in protein backbone is important in the protein backbone fragmentation due to the attack from reactive oxygen species (ROS). In this study, an alanine peptide was used model system to investigate this O-base oxidation by employing density functional theory (DFT) calculations combining with continuum solvent model. Detailed reaction steps were analyzed along with their reaction rate constants.

Site specificity of OH α-H abstraction reaction for a β-hairpin peptide: an ab initio study.

A β-hairpin peptide (PDB ID 1UAO) was modeled to explore the backbone oxidation of a protein by an OH radical to abstract one α-H atom with ab initio calculation at the B3LYB/6-31G(d) without any constraint. Three glycine residues located at three different sites in 1UAO were used to examine the possible site specificity of this backbone oxidation. The pre- and post-reactive complexes along with their associated transition states were located and verified by the intrinsic reaction coordinate method.

Antcin A, a steroid-like compound from Antrodia camphorata, exerts anti-inflammatory effect via mimicking glucocorticoids.

Aim: To determine the active ingredient of Niuchangchih (Antrodia camphorata) responsible for its anti-inflammatory effects and the relevant molecular mechanisms.

Methods: Five major antcins (A, B, C, H, and K) were isolated from fruiting bodies of Niuchangchih. Structural similarity between the antcins and 2 glucocorticoids (cortisone and dexamethasone) was compared.

Magnesium lithospermate B extracted from Salvia miltiorrhiza elevates intracellular Ca(2+) level in SH-SY5Y cells.

Aim: To examine if magnesium lithospermate B (MLB), a potent inhibitor of Na(+)/K(+)-ATPase, leads to the elevation of intracellular Ca(2+) level as observed in cells treated with cardiac glycosides.

Methods: Viability of SH-SY5Y neuroblastoma cells treated with various concentrations of ouabain or MLB was measured. Intracellular Ca(2+) levels were visualized using Fluo4-AM (fluorescent dye) when cells were treated with ouabain or MLB in the presence or absence of KB-R7943 (Na(+)/Ca(2+) exchanger inhibitor) and 2-APB (IP(3) receptor antagonist).

Steroid-like compounds in Chinese medicines promote blood circulation via inhibition of Na+/K+ -ATPase.

Aim: To examine if steroid-like compounds found in many Chinese medicinal products conventionally used for the promotion of blood circulation may act as active components via the same molecular mechanism triggered by cardiac glycosides, such as ouabain.

Methods: The inhibitory potency of ouabain and the identified steroid-like compounds on Na(+)/K(+)-ATPase activity was examined and compared. Molecular modeling was exhibited for the docking of these compounds to Na(+)/K(+)-ATPase.

Docking study of the precursor peptide of mastoparan onto its putative processing enzyme, dipeptidyl peptidase IV: a revisit to molecular ticketing.

Stepwise-cleavage process of promastoparans to reach maturity was investigated theoretically by combining ab initio folding and unbounded docking. The comparison between the structures of the promastoparans both before and after docking were examined along with the hydrogen bonding interaction pattern between the dipetidyl peptidase IV (DPPIV) and promastoparans to reveal how the endpoint of this stepwise cleavage is recognized among these promastoparans with highly resemble amino acid sequences. The current approach of folding and docking study provides structural insight on the stepwise cleavage process.

Variation of reaction dynamics for OH hydrogen abstraction from glycine between ab initio levels of theory.

The variation in reaction dynamics of OH hydrogen abstraction from glycine between HF, MP2, CCSD(T), M05-2X, BHandHLYP, and B3LYP levels was demonstrated. The abstraction mode shows distinct patterns between these five levels and determines the barrier height, and the spin density transfer between OH radical and glycine. These differences are mainly resulted from the spin density distribution and geometry of the alpha carbon during the abstraction.

Energy landscapes associated with the self-aggregation of an alanine-based oligopeptide (AAKA)4.

The alanine-based 16-mer peptide (AAKA)(4) has recently been shown to aggregate into a hydrogel at centimolar concentrations and high ionic strength ( Measey, T. J.; Schweitzer-Stenner, R.

Stability of artificial oil bodies constituted with recombinant caleosins.

Caleosin is a unique calcium binding protein anchoring to the surface of seed oil bodies by its central hydrophobic domain composed of an amphiphatic alpha-helix and a proline-knot subdomain. Stable artificial oil bodies were successfully constituted with recombinant caleosin overexpressed in Escherichia coli. The stability of artificial oil bodies was slightly or severely reduced when the amphiphatic alpha-helix or proline-knot subdomain in the hydrophobic domain of caleosin was truncated.

Effect of sugar positions in ginsenosides and their inhibitory potency on Na+/K+-ATPase activity.

Aim: To determine whether ginsenosides with various sugar attachments may act as active components responsible for the cardiac therapeutic effects of ginseng and sanqi (the roots of Panax ginseng and Panax notoginseng) via the same molecular mechanism triggered by cardiac glycosides, such as ouabain and digoxin.

Methods: The structural similarity between ginsenosides and ouabain was analyzed. The inhibitory potency of ginsenosides and ouabain on Na+/K+-ATPase activity was examined and compared.

Site specificity of the (alpha)C--H bond dissociation energy for a naturally occurring beta-hairpin peptide-An ab initio study.

A naturally occurring beta-hairpin peptide (PDB ID 1UAO) was used as a model to study the backbone oxidation of a protein with ab initio calculation at the B3LYB/6-31G(d) without any constraints. The (alpha)C--H bond dissociation energy of three different glycyl radicals located at different sites on the beta-hairpin peptide was calculated to evaluate the site specificity of backbone oxidation. The molecular and electronic structures of these glycyl radicals were analyzed to rationalize this site specificity.

Construction and comparison of fluorescence and bioluminescence bacterial biosensors for the detection of bioavailable toluene and related compounds.

Environmental pollution with petroleum products such as benzene, toluene, ethylbenzene, and xylenes (BTEX) has garnered increasing awareness because of its serious consequences for human health and the environment. We have constructed toluene bacterial biosensors comprised of two reporter genes, gfp and luxCDABE, characterized by green fluorescence and luminescence, respectively, and compared their abilities to detect bioavailable toluene and related compounds. The bacterial luminescence biosensor allowed faster and more-sensitive detection of toluene; the fluorescence biosensor strain was much more stable and thus more applicable for long-term exposure.

Magnesium lithospermate B possesses inhibitory activity on Na+,K+-ATPase and neuroprotective effects against ischemic stroke.

Aim: To examine if magnesium lithospermate B (MLB) extracted from Danshen, the dried roots of Salvia miltiorrhiza, may act as an active component responsible for the cardiac therapeutic effect of this traditional Chinese herb via the same molecular mechanism triggered by cardiac glycosides, such as ouabain and digoxin. Moreover, we wanted to test if MLB may provide neuroprotection against ischemic stroke as observed for cardiac glycosides.

Methods: Similarity in the chemical structure and molecular configuration between MLB and ouabain was analyzed.

Site specificity of alpha-H abstraction reaction among secondary structure motif--an ab initio study.

The initial step of protein oxidation is studied through alpha-H abstraction by an OH radical with various secondary structure motifs of proteins. It is found that there exist preferential alpha-Hs in this kind of abstractions. The typical abstraction mechanism involves three steps: forming a pre-reactive complex before abstraction, the abstraction reaction, and the H(2)O detachment from a post-reactive complex to form the product, C(alpha)-center radical.

Gene families encoding isoforms of two major sesame seed storage proteins, 11S globulin and 2S albumin.

Sesame (Sesamum indicum L.) seed has been recognized as a nutritional protein source owing to its richness in methionine. Storage proteins have been implicated in allergenic responses to sesame consumption.

Even-numbered metal chain complexes: synthesis, characterization, and DFT analysis of [Ni4(mu4-Tsdpda)4(H2O)2] (Tsdpda2- = N-(p-toluenesulfonyl)dipyridyldiamido), [Ni4(mu4-Tsdpda)4]+, and related Ni4 string complexes.

The synthesis and the X-ray structure of two complexes exhibiting a linear chain of four nickel atoms is reported, following Ni4(mu4-phdpda)4 (1), which had been characterized previously. [Ni4(mu4-Tsdpda)4(H2O)2], where H2Tsdpda is N-(p-toluenesulfonyl)dipyridyldiamine (2), is axially coordinated to two water molecules, at variance with 1. One-electron oxidation of 2 resulted in the loss of the axial ligands, yielding [Ni4(mu4-Tsdpda)4]+, [3]+, which was also structurally characterized.