Effects of force fields on the conformational and dynamic properties of amyloid β(1‐40) dimer explored by replica exchange molecular dynamics simulations

The conformational space and structural ensembles of amyloid beta (Aβ) peptides and their oligomers in solution are inherently disordered and proven to be challenging to study. Optimum force field selection for molecular dynamics (MD) simulations and the biophysical relevance of results are still unknown. We compared the conformational space of the Aβ(1‐40) dimers by 300 ns replica exchange MD simulations at physiological temperature (310 K) using: the AMBER‐ff99sb‐ILDN, AMBER‐ff99sb*‐ILDN, AMBER‐ff99sb‐NMR, and CHARMM22* force fields. Statistical comparisons of simulation results to experimental data and previously published simulations utilizing the CHARMM22* and CHARMM36 force fields were performed. All force fields yield sampled ensembles of conformations with collision cross sectional areas for the dimer that are statistically significantly larger than experimental results. All force fields, with the exception of AMBER‐ff99sb‐ILDN (8.8 ± 6.4%) and CHARMM36 (2.7 ± 4.2%), tend to overestimate the α‐helical content compared to experimental CD (5.3 ± 5.2%). Using the AMBER‐ff99sb‐NMR force field resulted in the greatest degree of variance (41.3 ± 12.9%). Except for the AMBER‐ff99sb‐NMR force field, the others tended to under estimate the expected amount of β‐sheet and over estimate the amount of turn/bend/random coil conformations. All force fields, with the exception AMBER‐ff99sb‐NMR, reproduce a theoretically expected β‐sheet‐turn‐β‐sheet conformational motif, however, only the CHARMM22* and CHARMM36 force fields yield results compatible with collapse of the central and C‐terminal hydrophobic cores from residues 17‐21 and 30‐36. Although analyses of essential subspace sampling showed only minor variations between force fields, secondary structures of lowest energy conformers are different.     

Fibroblast dynamics as an in vitro screening platform for anti‐fibrotic drugs in primary myelofibrosis

Although the cause for bone marrow fibrosis in patients with myelofibrosis remains controversial, it has been hypothesized that it is caused by extensive fibroblast proliferation under the influence of cytokines generated by the malignant megakaryocytes. Moreover, there is no known drug therapy which could reverse the process. We studied the fibroblasts in a novel system using the hanging drop method, evaluated whether the fibroblasts obtain from patients are part of the malignant clone of not and, using this system, we screen a large library of FDA‐approved drugs to identify potential drugs candidates that might be useful in the treatment of this disease, specifically which would inhibit fibroblast proliferation and the development of bone marrow fibrosis. We have found that the BM fibroblasts are not part of the malignant clone, as previously suspected and two immunosuppressive medications—cyclosporine and mycophenolate mophetil, as most potent suppressors of the fibroblast collagen production thus potentially inhibitors of bone marrow fibrosis production in myelofibrosis.     

Epidemiological analysis of serum anti‐Pseudomonas aeruginosa PcrV titers in adults

Of the various virulence mechanisms of the opportunistic pathogen Pseudomonas aeruginosa, the type III secretion system (TTSS) has been characterized as a major factor associated with acute lung injury, bacteremia and mortality. In addition, PcrV, a component protein of the TTSS, has been characterized as a protective antigen against infection with P. aeruginosa. This study comprised an epidemiological analysis of serum anti‐PcrV titers in a cohort of Japanese adults. From April 2012 to March 2013, serum anti‐PcrV titers of 198 volunteer participants undergoing anesthesia for scheduled surgeries were measured. The median, minimum and maximum serum anti‐PcrV titers among the 198 participants were 4.09 nM, 1.01 nM and 113.81 nM, respectively. The maximum peaks in the histogram were within the anti‐PcrV 2.00–4.99 nM titer range; values for 115 participants (58.1%) were within this range. Anti‐PcrV titers were more than approximately three‐fold greater (>12 nM) than the median value in 21 participants (10.6%). Ten‐year interval age increases, history of treatment for traffic trauma, and a history of past surgery each showed statistically significant associations with higher anti‐PcrV titers (i.e., >10 nM) than did the other factors assessed by binomial analysis. This study revealed a considerable variation in anti‐PcrV titers in adult subjects without any obvious histories of infection with P. aeruginosa.     

Testing hypotheses about the function of repeated nest abandonment as a life history strategy in a passerine bird

Nest structures are essential for successful reproduction in most bird species. Nest construction costs time and energy, and most bird species typically build one nest per breeding attempt. Some species, however, build more than one nest, and the reason for this behaviour is often unclear. In the Grey Fantail Rhipidura albiscapa, nest abandonment before egg‐laying is very common. Fantails will build up to seven nests within a breeding season, and pairs abandon up to 71% of their nests before egg‐laying. We describe multiple nest‐building behaviour in the Grey Fantail and test four hypotheses explaining nest abandonment in this species: cryptic depredation, destruction of nests during storm events, and two anti‐predatory responses (construction of decoy nests to confuse predators, and increasing concealment to ‘hide’ nests more effectively). We found support for only one hypothesis – that abandonment is related to nest concealment. Abandoned nests were significantly less concealed than nests that received eggs. Most abandoned nests were not completely built and none received eggs, thus ruling out cryptic predation. Nests were not more likely to be abandoned following storm events. The decoy nest hypothesis was refuted as abandoned nests were constructed at any point during the breeding season and some nests were dismantled and the material used to build the subsequent nest. Thus, Grey Fantails are flexible about nest‐site locations during the nest‐building phase and readily abandon nest locations if they are found to have deficient security.     

Recruitment of TBK1 to cytosol‐invading Salmonella induces WIPI2‐dependent antibacterial autophagy

Mammalian cells deploy autophagy to defend their cytosol against bacterial invaders. Anti‐bacterial autophagy relies on the core autophagy machinery, cargo receptors, and “eat‐me” signals such as galectin‐8 and ubiquitin that label bacteria as autophagy cargo. Anti‐bacterial autophagy also requires the kinase TBK1, whose role in autophagy has remained enigmatic. Here we show that recruitment of WIPI2, itself essential for anti‐bacterial autophagy, is dependent on the localization of catalytically active TBK1 to the vicinity of cytosolic bacteria. Experimental manipulation of TBK1 recruitment revealed that engagement of TBK1 with any of a variety of Salmonella‐associated “eat‐me” signals, including host‐derived glycans and K48‐ and K63‐linked ubiquitin chains, suffices to restrict bacterial proliferation. Promiscuity in recruiting TBK1 via independent signals may buffer TBK1 functionality from potential bacterial antagonism and thus be of evolutionary advantage to the host.     

Homobrassinolide induced conformational changes in hexokinase: a possible mechanism for its antidiabetic potential

Hormonal regulation of cell growth and development, tissue morphology, metabolism and physiological function in animals and man is a well‐established knowledge domain in modern biological science. The present study was carried out to investigate the structural stability of hexokinase when exposed to diabetic levels of glucose and its binding efficiency. The fluorescence study indicated that 28‐homobrassinolide was able to protect or restore the native structure of hexokinase. Proteins are synthesized and fold into the native form to become active. The inability of a protein molecule to remain in its native form is called as protein misfolding and this is because of several factors. Protein aggregation and misfolding are known to play a critical role in several human diseases including diabetes. Homobrassinolide interaction with hexokinase was studied by UV–Vis spectrophotometer and fluorescence spectrophotometer. Results were suggested that the denatured hexokinase was renatured upon binding with homobrassinolide. In silico, docking study was performed to recognize the binding activity of homobrassinolide against a subunit of the glucokinase, and homobrassinolide was able to bind to the drug binding pocket of glucokinase. The glide energy is ?7.1 kcal/mol, suggesting the high binding affinity of homobrassinolide to glucokinase. Overall, these studies predict that the phytohormone 28‐homobrassinolide would function as an anti‐diabetic when present in human and animal diet by augmenting the hexokinase enzyme activity in the animal cell. Copyright © 2015 John Wiley & Sons, Ltd.     

罗藦科马利筋亚科马利筋族植物C_(21)甾类成分研究进展

本文综述了 :到目前为止 ,从马利筋族植物中发现的 C2 1甾类成分及其分布 ,并介绍了一些化合物的药理作用。     

Non‐surgical method for the induction of delayed implantation and recovery of viable blastocysts in rats and mice by the use of tamoxifen and Depo‐Provera

Implantational delay in rats and mice is experimentally induced by withdrawal of oestrogen and maintenance of progesterone. The oestrogen is normally removed by ovariectomy. We report here that the use of the antioestrogenic effect of the drug tamoxifen in combination with Depo‐Provera (which counteracts the oestrogenic effects of the tamoxifen) may be used to put the embryos both of rats and mice into delay of implantation. These delayed embryos retain their developmental potential and give rise to live born young when transferred to pseudopregnant recipient females. They are a good source of ES cells. Mol. Reprod. Dev. 52:29–32, 1999. © 1999 Wiley‐Liss, Inc.