Evolution of domain combinations in protein kinases and its implications for functional diversity

Protein kinases phosphorylating Ser/Thr/Tyr residues in several cellular proteins exert tight control over their biological functions. They constitute the largest protein family in most eukaryotic species. Protein kinases classified based on sequence similarity in their catalytic domains, cluster into subfamilies, which share gross functional properties. Many protein kinases are associated or tethered covalently to domains that serve as adapter or regulatory modules,naiding substrate recruitment, specificity, and also serve as scaffolds. Hence the modular organisation of the protein kinases serves as guidelines to their functional and molecular properties. Analysis of genomic repertoires of protein kinases in eukaryotes have revealed wide spectrum of domain organisation across various subfamilies of kinases. Occurrence of organism-specific novel domain combinations suggests functional diversity achieved by protein kinases in order to regulate variety of biological processes. In addition, domain architecture of protein kinases revealed existence of hybrid protein kinase subfamilies and their emerging roles in the signaling of eukaryotic organisms. In this review we discuss the repertoire of non-kinase domains tethered to multi-domain kinases in the metazoans. Similarities and differences in the domain architectures of protein kinases in these organisms indicate conserved and unique features that are critical to functional specialization. (C) 2009 Elsevier Ltd. All rights reserved.

Existence and approximations of solutions to some fractional order functional integral equations

In this paper we shall study a fractional order functional integral equation. In the first part of the paper, we proved the existence and uniqueness of mile and global solutions in a Banach space. In the second part of the paper, we used the analytic semigroups theory oflinear operators and the fixed point method to establish the existence, uniqueness and convergence of approximate solutions of the given problem in a separable Hilbert space. We also proved the existence and convergence of Faedo-Galerkin approximate solution to the given problem. Finally, we give an example.

Metabolism of ubiquinone in relation to vitamin a status in the rat

1. 1. Biosynthetic experiments in vitro with slices of livers from normal and vitamin A-deficient rats confirmed that synthesis of ubiquinone did not increase in vitamin A deficiency. 2. 2. During development of deficiency of vitamin A in the rat, there was a definite increase in the synthesis of ubiquinone at the 10-days stage but this reverted to low, initial level by 20 days and after. 3. 3. Vitamin A analogues, 3-dehydroretinal, 5,6-monoepoxyretinal and retinoic acid, which supported growth have restored ubiquinone concentration to the normal levels and relieved the lowering in its catabolism. The biologically inert 5,8-monoepoxyretinal was the least active of the analogues tested. 4. 4. The concentration and synthesis of ubiquinone in the liver decreased under conditions of hypervitaminosis A. 5. 5. The experimental evidence does not support the hypothesis of inverse relationship between vitamin A and ubiquinone synthesis.

Vitamin C status of vitamin A-deficient rats

IT was initially suggested that vitamin A-deficiency leads to an interference in the biosynthesis of ascorbic acid, because depletion of vitamin A was found to cause a fall in the tissue-levels of ascorbate and diminished urinary ascorbic acid excretion in animals1-3. Mapson4, however, concluded that lowered ascorbic acid-levels in vitamin A-deficient rats is due to inanition only, because he was able to show that following chloretone treatment vitamin A-deficient and pair-fed vitamin A normal rats excrete comparable amounts of ascorbic acid in their urine and that restriction of food intake reduces the urinary ascorbate even in the chloretone-treated normal rats. Results of our preliminary experiments reported here clearly indicate that the synthesis of ascorbic acid in rats is markedly reduced during vitamin A-deficiency.

X-ray Crystallographic Analysis of the Complexes of Enoyl Acyl Carrier Protein Reductase of Plasmodium falciparum with Triclosan Variants to Elucidate the Importance of Different Functional Groups in Enzyme Inhibition

Triclosan, a well-known inhibitor of Enoyl Acyl Carrier Protein Reductase (ENR) from several pathogenic organisms, is a promising lead compound to design effective drugs. We have solved the X-ray crystal structures of Plasmodium falciparum ENR in complex with triclosan variants having different substituted and unsubstituted groups at different key functional locations. The structures revealed that 4 and 2' substituted compounds have more interactions with the protein, cofactor, and solvents when compared with triclosan. New water molecules were found to interact with some of these inhibitors. Substitution at the 2' position of triclosan caused the relocation of a conserved water molecule, leading to an additional hydrogen bond with the inhibitor. This observation can help in conserved water-based inhibitor design. 2' and 4' unsubstituted compounds showed a movement away from the hydrophobic pocket to compensate for the interactions made by the halogen groups of triclosan. This compound also makes additional interactions with the protein and cofactor which compensate for the lost interactions due to the unsubstitution at 2' and 4'. In cell culture, this inhibitor shows less potency, which indicates that the chlorines at 2' and 4' positions increase the ability of the inhibitor to cross multilayered membranes. This knowledge helps us to modify the different functional groups of triclosan to get more potent inhibitors. (C) 2010 IUBMB IUBMB Life, 62(6): 467-476.

Electronic phase separation in correlated oxides: The phenomenon, its present status and future prospects

Many transition metal oxide materials of high chemical purity are not necessarily monophasic. Thus, single crystals of chemically pure rare earth manganites and cobaltates of the general formula Ln1-xAxMO3 (Ln=rare earth metal, A=alkaline earth metal, M=Mn, Co) exhibit the phenomenon of electronic phase separation wherein phases of different electronic and magnetic properties coexist. Such phase separation, the length scale of which can vary anywhere between a few nanometers to microns, gives distinct signatures in X-ray and neutron diffraction patterns, electrical and magnetic properties, as well as in NMR and other spectroscopies. While the probe one employs to investigate electronic phase separation depends on the length scale, it is noteworthy that direct imaging of the inhomogeneities has been accomplished. Some understanding of this phenomenon has been possible on the basis of some of the theoretical models, but we are far from unraveling the varied aspects of this new phenomenon. Herein, we present the highlights of experimental techniques and theoretical approaches, and comment on the future outlook for this fascinating phenomenon

Hexagonally ordered arrays of metallic nanodots from thin films of functional block copolymers

We demonstrate a new and simple route to fabricate highly dense arrays of hexagonally close packed inorganic nanodots using functional diblock copolymer (PS-b-P4VP) thin films. The deposition of pre-synthesized inorganic nanoparticles selectively into the P4VP domains of PS-b-P4VP thin films, followed by removal of the polymer, led to highly ordered metallic patterns identical to the order of the starting thin film. Examples of Au, Pt and Pd nanodot arrays are presented. The affinity of the different metal nanoparticles towards P4VP chains is also understood by extending this approach to PS-b-P4VP micellar thin films. The procedure used here is simple, eco-friendly, and compatible with the existing silicon-based technology. Also the method could be applied to various other block copolymer morphologies for generating 1-dimensional (1D) and 2-dimensional (2D) structures. (c) 2010 Elsevier Ltd. All rights reserved.

PROMIDS: A PROtotype multi-rIng data flow system for functional programming languages

This paper presents a detailed description of the hardware design and implementation of PROMIDS: a PROtotype Multi-rIng Data flow System for functional programming languages. The hardware constraints and the design trade-offs are discussed. The design of the functional units is described in detail. Finally, we report our experience with PROMIDS.

Dynamic changes in mitogen-activated protein kinase (MAPK) activities in the corpus luteum of the bonnet monkey (Macaca radiata) during development, induced luteolysis, and simulated early pregnancy: A role for p38 MAPK in the regulation of luteal function

Changes in MAPK activities were examined in the corpus luteum (CL) during luteolysis and pregnancy, employing GnRH antagonist (Cetrorelix)-induced luteolysis, stages of CL, and hCG treatment to mimic early pregnancy as model systems in the bonnet monkey. We hypothesized that MAPKs could serve to phosphorylate critical phosphoproteins to regulate luteal function. Analysis of several indices for structural (caspase-3 activity and DNA fragmentation) and functional (progesterone and steroidogenic acute regulatory protein expression) changes in the CL revealed that the decreased luteal function observed during Cetrorelix treatment and late luteal phase was associated with increased caspase-3 activity and DNA fragmentation. As expected, human chorionic gonadotropin treatment dramatically increased luteal function, but the indices for structural changes were only partially attenuated. All three MAPKs appeared to be constitutively active in the mid-luteal-phase CL, and activities of ERK-1/2 and p38-MAPK (p38), but not Jun N-terminal kinase (JNK)-1/2, decreased significantly (P < 0.05) within 12 - 24 h after Cetrorelix treatment. During the late luteal phase, in contrast to decreased ERK-1/2 and p38 activities, JNK-1/2 activities increased significantly (P < 0.05). Although human chorionic gonadotropin treatment increased ERK-1/2 and p38 activities, it decreased JNK-1/2 activities. The activation status of p38 was correlated with the phosphorylation status of an upstream activator, MAPK kinase-3/6 and the expression of MAPK activated protein kinase-3, a downstream target. Intraluteal administration of p38 kinase inhibitor (SB203580), but not MAPK kinase-1/2 inhibitor (PD98059), decreased the luteal function. Together, these data suggest an important role for p38 in the regulation of CL function in primates.

Hydrolysis of Organophosphate Esters: Phosphotriesterase Activity of Metallo-beta-lactamase and Its Functional Mimics

The phosphotriesterase (PTE) activity of a series of binuclear and mononuclear zinc(II) complexes and metallo-beta-lactamase (m beta 1) from Bacillus cereus was studied. The binuclear complex 1, which exhibits good m beta 1 activity, shows poor PTE activity. In contrast,complex 2, a poor mimic of m beta 1, exhibits much higher activity than 1 The replacement of Cl- ligands by OH- is important for the high PTE activity of complex 2 because this complex does not show any catalytic activity in methanol. The natural enzyme m beta 1 from B. cereus is also found to be an inefficient catalyst in the hydrolysis of phosphotriesters. These observations indicate that the binding of beta-lactam substrates at the binuclear zinc(II) center is different from that of phosphotriesters. Furthermore, phosphodiesters, the products from the hydrolysis of triesters, significantly inhibit the PTE activity of m beta 1 and its functional mimics. Although the mononuclear complexes 3 and 4 exhibited significant m beta 1 activity, these complexes are found to be almost inactive in the hydrolysis of phosphotriesters. These observations indicate that the elimination of phosphodiesters from the reaction site is important for the PTE activity of zinc(II) complexes.

Functional linkages can reveal protein complexes for structure determination

The study of molecular machines, and protein complexes in general, is a growth area of biology. Is there a computational method for inferring which combinations of proteins in an organism are likely to form a crystallizable complex? We use the Protein Data Bank (PDB) to assess the usefulness of inferred functional protein linkages for this task. We find that of 242 nonredundant prokaryotic protein complexes (complexes excluding structural variants of the same protein) from organisms that are shared between the current PDB and the Prolinks functional linkage database, 44% (107/242) contain proteins that are linked at high-confidence by one or more methods of computed functional linkages. This suggests that computing functional linkages will be useful in defining protein complexes for structural studies. We offer a database of such inferred linkages corresponding to likely protein complexes for some 629,952 pairs of proteins in 154 prokaryotes and archea.