The role of lysine-41 in RNase A catalysis - A quantum chemical study on the active site ligand complex

Several mechanisms have been proposed to explain the action of enzymes at the atomic level. Among them, the recent proposals involving short hydrogen bonds as a step in catalysis by Gerlt and Gassman [1] and proton transfer through low barrier hydrogen bonds (LBHBs) [2, 3] have attracted attention. There are several limitations to experimentally testing such hypotheses, Recent developments in computational methods facilitate the study of active site-ligand complexes to high levels of accuracy, Our previous studies, which involved the docking of the dinucleotide substrate UpA to the active site of RNase A [4, 5], enabled us to obtain a realistic model of the ligand-bound active site of RNase A. From these studies, based on empirical potential functions, we were able to obtain the molecular dynamics averaged coordinates of RNase A, bound to the ligand UpA. A quantum mechanical study is required to investigate the catalytic process which involves the cleavage and formation of covalent bonds. In the present study, we have investigated the strengths of some of the hydrogen bonds between the active site residues of RNase A and UpA at the ab initio quantum chemical level using the molecular dynamics averaged coordinates as the starting point. The 49 atom system and other model systems were optimized at the 3-21G level and the energies of the optimized systems were obtained at the 6-31G* level. The results clearly indicate the strengthening of hydrogen bonds between neutral residues due to the presence of charged species at appropriate positions. Such a strengthening manifests itself in the form of short hydrogen bonds and a low barrier for proton transfer. In the present study, the proton transfer between the 2'-OH of ribose (from the substrate) and the imidazole group from the H12 of RNase A is influenced by K41, which plays a crucial role in strengthening the neutral hydrogen bond, reducing the barrier for proton transfer.

Constrained linear filter and its relation to singular optimal control

This paper presents an analysis of an optimal linear filter in the presence of constraints on the moan squared values of the estimates from the viewpoint of singular optimal control. The singular arc has been shown to satisfy the generalized Legcndrc-Clebseh condition and Jacobson's condition. Both the cases of white measurement noise and coloured measurement noise are considered. The constrained estimate is shown to be a linear transformation of the unconstrained Kalman estimate.

Reversible cation/anion extraction from K2La2Ti3O10: Formation of new layered titanates, KLa2Ti3O9.5 and La2Ti3O9

A new soft-chemical transformation of layered perovskite oxides is described wherein K2O is sequentially extracted from the Ruddlesden-Popper (R-P) phase, K2La2Ti3O10 (I), yielding novel anion-deficient KLa2Ti3O9.5 (II) and La2Ti3O9 (III). The transformation occurs in topochemical reactions of the R-P phase I with PPh4Br and PBu4Br (Ph = phenyl; Bu = n-butyl). The mechanism involves the elimination of KBr accompanied by decomposition of PR4+ (R = phenyl or n-butyl) that extracts oxygen from the titanate. Analysis of the organic products of decomposition reveals formation of Ph3PO, Ph3P, and Ph-Ph for R = phenyl, and Bu3PO, Bu3P along with butane, butene, and octane for R = butyl. The inorganic oxides II and III crystallize in tetragonal structures (II: P4/mmm, a = 3.8335(1) angstrom, c = 14.334(1) angstrom; III: /4/ mmm, a = 3.8565(2) angstrom, c = 24.645(2) angstrom) that are related to the parent R-P phase. II is isotypic with the Dion-Jacobson phase, RbSr2Nb3O10, while III is a unique layered oxide consisting of charge-neutral La2Ti3O9 anion-deficient perovskite sheets stacked one over the other without interlayer cations. Interestingly, both II and III convert back to the parent R-P phase in a reaction with KNO3. While transformations of the R-P phases to other related layered/three-dimensional perovskite oxides in ion-exchange/metathesis/dehydration/reduction reactions are known, the simultaneous and reversible extraction of both cations and anions in the conversions K2La2Ti3O10 reversible arrow KLa2Ti3O9.5 reversible arrow La2Ti3O9 is reported here for the first time.

A[Bi3Ti4O13] and A[Bi3PbTi5O16] (A = K, Cs): New n=4 and n=5 members of the layered perovskite series, A[A ' n-1B nO3n+1], and their hydrates

We describe the synthesis and structural characterization of new layered bismuth titanates, A[Bi3Ti4O13] and A[Bi3PbTi5O16]for A = K, Cs, corresponding to n = 4 and 5 members of the Dion-Jacobson series of layered perovskites of the general formula, A[A'n-1BnO3n+1]. These materials have been prepared by solid state reaction of the constituents containing excess alkali, which is required to suppress the formation of competitive Aurivillius phases. Unlike the isostructural niobates and niobium titanates of the same series, the new phases reported here are spontaneously hydrated-a feature which could make them potentially useful as photocatalysts for water splitting reaction. On hydration of the potassium compounds, the c axis expands by ca. 2 Angstrom and loses its doubling [for example, the tetragonal lattice parameters of K[Bi3Ti4O13] and its dihydrate are respectively a = 3900(1)Angstrom c 37.57(2) Angstrom; a 3.885(1) Angstrom, c = 20.82(4) Angstrom]; surprisingly, the cesium analogues do not show a similar change on hydration.

Direct detection of Salmonella without pre-enrichment in milk, ice-cream and fruit juice by PCR against hilA gene

A novel PCR based assay was devised to specifically detect contamination of any Salmonella serovar in milk, fruit juice and ice-cream without pre-enrichment. This method utilizes primers against hilA gene which is conserved in all Salmonella serovars and absent from the close relatives of Salmonella. An optimized protocol, in terms time and money, is provided for the reduction of PCR contaminants from milk, ice-cream and juice through the use of routine laboratory chemicals. The simplicity, efficiency (time taken 3-4 h) and sensitivity (to about 5-10 CFU/ml) of this technique confers a unique advantage over other previously used time consuming detection techniques. This technique does not involve pre-enrichment of the samples or extensive sample processing, which was a pre-requisite in most of the other reported studies. Hence, this assay can be ideal for adoption, after further fine tuning, by food quality control for timely detection of Salmonella contamination as well as other food-borne pathogens (with species specific primers) in food especially milk, ice-cream and fruit juice. (C) 2011 Elsevier Ltd. All rights reserved.

MicroRNA-155 Is Required for Mycobacterium bovis BCG-Mediated Apoptosis of Macrophages

Pathogenic rnycobacteria, including Mycobacterium tuberculosis and Mycobacterium bovis, cause significant morbidity and mortality worldwide. However, the vaccine strain Mycobacterium bovis BCG, unlike virulent strains, triggers extensive apoptosis of infected macrophages, a step necessary for the elicitation of robust protective immunity. We here demonstrate that M. bovis BCG triggers Toll-like receptor 2 (TLR2)-dependent microRNA-155 (miR-155) expression, which involves signaling cross talk among phosphatidylinositol 3-kinase (PI3K), protein kinase C delta (PKC delta), and mitogen-activated protein kinases (MAPKs) and recruitment of NF-kappa B and c-ETS to miR-155 promoter. Genetic and signaling perturbations presented the evidence that miR-155 regulates PKA signaling by directly targeting a negative regulator of PKA, protein kinase inhibitor alpha (PKI-alpha). Enhanced activation of PKA signaling resulted in the generation of PKA C-alpha; phosphorylation of MSK1, cyclic AMP response element binding protein (CREB), and histone H3; and recruitment of phospho-CREB to the apoptotic gene promoters. The miR-155-triggered activation of caspase-3, BAK1, and cytochrome c translocation involved signaling integration of MAPKs and epigenetic or posttranslational modification of histones or CREB. Importantly, M. bovis BCG infection-induced apoptosis was severely compromised in macrophages derived from miR-155 knockout mice. Gain-of-function and loss-of-function studies validated the requirement of miR-155 for M. bovis BCG's ability to trigger apoptosis. Overall, M. bovis BCG-driven miR-155 dictates cell fate decisions of infected macrophages, strongly implicating a novel role for miR-155 in orchestrating cellular reprogramming during immune responses to mycobacterial infection.

CTFS-ForestGEO: a worldwide network monitoring forests in an era of global change

Global change is impacting forests worldwide, threatening biodiversity and ecosystem services including climate regulation. Understanding how forests respond is critical to forest conservation and climate protection. This review describes an international network of 59 long-term forest dynamics research sites (CTFS-ForestGEO) useful for characterizing forest responses to global change. Within very large plots (median size 25ha), all stems 1cm diameter are identified to species, mapped, and regularly recensused according to standardized protocols. CTFS-ForestGEO spans 25 degrees S-61 degrees N latitude, is generally representative of the range of bioclimatic, edaphic, and topographic conditions experienced by forests worldwide, and is the only forest monitoring network that applies a standardized protocol to each of the world's major forest biomes. Supplementary standardized measurements at subsets of the sites provide additional information on plants, animals, and ecosystem and environmental variables. CTFS-ForestGEO sites are experiencing multifaceted anthropogenic global change pressures including warming (average 0.61 degrees C), changes in precipitation (up to +/- 30% change), atmospheric deposition of nitrogen and sulfur compounds (up to 3.8g Nm(-2)yr(-1) and 3.1g Sm(-2)yr(-1)), and forest fragmentation in the surrounding landscape (up to 88% reduced tree cover within 5km). The broad suite of measurements made at CTFS-ForestGEO sites makes it possible to investigate the complex ways in which global change is impacting forest dynamics. Ongoing research across the CTFS-ForestGEO network is yielding insights into how and why the forests are changing, and continued monitoring will provide vital contributions to understanding worldwide forest diversity and dynamics in an era of global change.