Molecular insights into the mechanisms of cation-type specific stability and denaturation of poly-l-glutamate: a simulation study

Cation-induced conformational changes of peptide as a guide to developing insights into human diseases-related proteins have received a lot of attention. The interactions between poly-l-glutamate (PGA) and different cations, including Na⁺, K⁺ and Mg²⁺, respectively, are studied in solvent at a concentration of 1 M, and the behaviours of peptide with different cations are investigated. For Na⁺, an oscillatory stabilising process to α-helix PGA is found, in accordance with the uniform free-energy landscape, whereas for K⁺, an extended α-helix structure is formed by the terminal turns, suggesting a weaker attraction to charged head groups. For Mg²⁺, the bridged charged side chains are responsible for the maximum probability of helix state. These distinct structural changes can be attributed to the different interactions between charged head groups and cations. Both Na⁺ and K⁺ are mainly attracted around head groups by direct ion binding while Mg²⁺ is centrally trapped among adjacent charged head groups. In addition, a surprising shift of the backbone hydrogen bond, from intact state to intermediate state, is observed. This is opposite to the stabilising effect of Na⁺ around negatively charged head groups.     

Studies of ice melting using molecular dynamics

In this paper, the melting of ice 1h is studied using molecular dynamics (MD). Common potential functions employed in the MD simulations include SPC/E, TIP4P, TIP5P, TIP4/ice and TIP5P/E. We first conducted melting of ice bulks and then studied the melting speed of the ice/water interface during ice melting. It is found that various potentials result in similar ice-melting phenomena. The result is compared with the analytical solution for phase change problem. We also studied size effects and temperature gradient effects on ice melting.     

A novel model for the molecular dynamics simulation study on mechanical properties of HMX/F2311 polymer-bonded explosive

The ‘insert’ model for β-octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX)-based polymer-bonded explosive (PBX) was proposed for finding the relation of temperatures with mechanical properties. This model was simulated by using molecular dynamics models. The elastic constants and the effective moduli were calculated with static analysis method. Cauchy pressure was also calculated. It is found that the rigidity is weakened and the ductibility is improved by adding a small amount of F₂₃₁₁ in the crystalline HMX. The rigidity is also weakened with increasing temperature. However, the ductibility of HMX/F₂₃₁₁ PBX changes as a parabola with increasing temperature duo to the enhancement of F₂₃₁₁ molecular chain movement and simultaneously the increment of high energy conformation ratio in this molecular chain, i.e. the increment of the molecular chain rigidity.     

Involvement of Volume-Activated Chloride Channels in H2O2 Preconditioning Against Oxidant-Induced Injury Through Modulating Cell Volume Regulation Mechanisms and Membrane Permeability in PC12 Cells

The functions of chloride channels in preconditioning-induced cell protection remain unclear. In this report, we show that the volume-activated chloride channels play a key role in hydrogen peroxide (H₂O₂) preconditioning-induced cell protection in pheochromocytoma PC12 cells. The preconditioning with 100 μM H₂O₂ for 90 min protected the cells from injury induced by long period exposure to 300 μM H₂O₂. The protective effect was attenuated by pretreatment with the chloride channel blockers, 5-nitro-2-3-phenylpropylamino benzoic acid (NPPB) and tamoxifen. H₂O₂ preconditioning directly activated a chloride current, which was moderately outward-rectified and sensitive to the chloride channel blockers and hypertonicity-induced cell shrinkage. H₂O₂ preconditioning functionally up-regulated the activities of volume-activated chloride channels and enhanced the regulatory volume decrease when exposure to extracellular hypotonic challenges. In addition, acute application of H₂O₂ showed distinctive actions on cell volume and membrane permeability in H₂O₂ preconditioned cells. In H₂O₂ preconditioned cells, acute application of 300 μM H₂O₂ first promptly induced a decrease of cell volume and enhancement of cell membrane permeability, and then, cell volume was maintained at a relatively stable level and the facilitation of membrane permeability was reduced. Conversely, in control cells, 300 μM H₂O₂ induced a slow but persistent apoptotic volume decrease (AVD) and facilitation of membrane permeability. H₂O₂ preconditioning also significantly up-regulated the expression of ClC-3 protein, the molecular candidate of the volume-activated chloride channel. These results suggest that H₂O₂ preconditioning can enhance the expression and functional activities of volume-activated chloride channels, thereby modulate cell volume and cell membrane permeability, which may contribute to neuroprotection against oxidant-induced injury.     

Structural basis of calcineurin activation by calmodulin

Calcineurin is the only known calmodulin (CaM) activated protein phosphatase, which is involved in the regulation of numerous cellular and developmental processes and in calcium-dependent signal transduction. Although commonly assumed that CaM displaces the autoinhibitory domain (AID) blocking substrate access to its active site, the structural basis underlying activation remains elusive. We have created a fused ternary complex (CBA) by covalently linking three polypeptides: CaM, calcineurin regulatory B subunit (CnB) and calcineurin catalytic A subunit (CnA). CBA catalytic activity is comparable to that of fully activated native calcineurin in the presence of CaM. The crystal structure showed virtually no structural change in the active site and no evidence of CaM despite being covalently linked. The asymmetric unit contains four molecules; two parallel CBA pairs are packed in an antiparallel mode and the large cavities in crystal packing near the calcineurin active site would easily accommodate multiple positions of AID-bound CaM. Intriguingly, the conformation of the ordered segment of AID is not altered by CaM; thus, it is the disordered part of AID, which resumes a regular α-helical conformation upon binding to CaM, which is displaced by CaM for activation. We propose that the structural basis of calcineurin activation by CaM is through displacement of the disordered fragment of AID which otherwise impedes active site access.     

DNA methylation and MeCP2 regulation of PTCH1 expression during rats hepatic fibrosis

Hepatic stellate cell (HSC) activation plays an important role in liver fibrogenesis. Transdifferentiation of quiescent hepatic stellate cells into myofibroblastic-HSCs is a key event in liver fibrosis. The methyl-CpG-binding protein MeCP2 which promotes repressed chromatin structure is selectively detected in myofibroblasts of diseased liver. MeCP2 binds to methylated CpG dinucleotides, which are abundant in the promoters of many genes. Treatment of HSCs with DNA methylation inhibitor 5-aza-2′- deoxycytidine (5-azadC) prevented proliferation and activation. Treatment with 5-azadC prevented loss of Patched (PTCH1) expression that occurred during HSCs activation. In a search for underlying molecular medchanisms, we investigated whether the targeting of epigenetic silencing mechanisms could be useful in the treatment of PTCH1-associated fibrogenesis. It was indicated that hypermethylation of PTCH1 is associated with the perpetuation of fibroblast activation and fibrosis in the liver. siRNA knockdown of MeCP2 increased the expressions of PTCH1 mRNA and protein in hepatic myofibroblasts. These data suggest that DNA methylation and MeCP2 may provide molecular mechanisms for silencing of PTCH1.     

Enantioselective Uptake and Translocation of a Novel Chiral Neonicotinoid Insecticide Cycloxaprid in Youdonger (Brassica campestris subsp. Chinensis)

For a novel potential commercial chiral pesticide, an independent study on the fate characteristics and residues of each stereoisomer is essential if the application rates for the pesticide and human exposure are to be reduced. The absorption and translocation behavior of a chiral insecticide, cycloxaprid, in plants treated by root immersion and blade smearing was studied using ¹⁴C‐labeling tracer techniques. With the root treatment, total absorption of (1R;8S)‐cycloxaprid (RS) (12.39%) was much greater than that of (1S;8R)‐cycloxaprid (SR) (3.31%) at 192 h after treatment (HAT). The mass concentrations ( RS / SR ) of cycloxaprid in the roots, cotyledons, leaf 1, leaf 2, and leaf 3 were 37.0/16.8, 8.3/2.8, 11.7/6.5, 5.1/4.8, and 8.0/4.7 mg kg^‐1 (fresh weight), respectively, at 192 HAT at an initial concentration 1.6 mg kg^‐1. With the foliar application treatment, no significant difference was observed between the total absorption of RS (3.11%) and SR (4.03%) at the end of the treatment. Both acropetal and basipetal transport of absorbed ¹⁴C occurred and more than 71.83% of absorbed RS and 82.42% of SR remained in the treated leaf. Stereoselective absorption was observed during root uptake but not during foliar absorption. Chirality 25:686–691, 2013. © 2013 Wiley Periodicals, Inc.     

Analysis of B-Class Genes NAP3L3 and NAP3L4 in Narcissus tazetta var. chinensis

Very few flower organ identity genes have been characterized in Chinese narcissus (Narcissus tazetta var. chinensis), which has petaloid sepals. Here, we report the cloning of two full-length B-class genes, namely NAP3L3 and NAP3L4, that are orthologs of the DEFICIENS lineage. Both genes are highly expressed in the second whorl of the perianth and in the stamens. NAP3L4 is also expressed strongly in the ovule. The functions of these two genes were further analyzed using transgenic plants. Ectopic expression of either gene in Arabidopsis gave no obvious floral organ transformation phenotypes. In yeast two-hybrid assays, NAP3L3 and NAP3L4 failed to homodimerize and interacted weakly with each other. The data suggest that these two genes might not be involved in the formation of petaloid sepals. Isolation and functional analysis of other B-class paralogs should be conducted to fully understand petaloid tepal development in Chinese narcissus.     

Branched Nanowire Based Guanine Rich Oligonucleotides

Abstract

Self-assembly and aggregation of guanine rich sequences can provide useful insights into DNA nanotechnology and telomeric structure and function. In this paper, we designed a guanine rich sequence d(GGCGTTTTGCGG). We found that it can form stable structure in appropriate condition and it exhibits an anomalous CD spectra. This structures can be imaged in ambient environment with a Nanoscope III AFM (Digital Instruments). We found it forms branch structure and long multistrand DNA nanowire after incubation at 37°C for 612 hours in 25 mM TE (pH=8.0) + 5 mM Mg²⁺ + 50 mM K⁺. The ability to self-assemble into branches and long wires not only clearly demonstrate its potential as scaffold structures for nanotechnology, but also give aids to understand telomeric structure further. We have proposed a model to explain how these structures formed.