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.

Analysis of connectivity map: Control to glutamate injured and phenobarbital treated neuronal network

We study the responses of a cultured neural network when it is exposed to epileptogenesis glutamate injury causing epilepsy and subsequent treatment with phenobarbital by constructing connectivity map of neurons using correlation matrix. This study is particularly useful in understanding the pharmaceutical drug induced changes in the neuronal network properties with insights into changes at the systems biology level. (C) 2010 American Institute of Physics. [doi:10.1063/1.3398025]

Comparative analysis of thermophilic and mesophilic proteins using Protein Energy Networks

Background: Thermophilic proteins sustain themselves and function at higher temperatures. Despite their structural and functional similarities with their mesophilic homologues, they show enhanced stability. Various comparative studies at genomic, protein sequence and structure levels, and experimental works highlight the different factors and dominant interacting forces contributing to this increased stability. Methods: In this comparative structure based study, we have used interaction energies between amino acids, to generate structure networks called as Protein Energy Networks (PENs). These PENs are used to compute network, sub-graph, and node specific parameters. These parameters are then compared between the thermophile-mesophile homologues. Results: The results show an increased number of clusters and low energy cliques in thermophiles as the main contributing factors for their enhanced stability. Further more, we see an increase in the number of hubs in thermophiles. We also observe no community of electrostatic cliques forming in PENs. Conclusion: In this study we were able to take an energy based network approach, to identify the factors responsible for enhanced stability of thermophiles, by comparative analysis. We were able to point out that the sub-graph parameters are the prominent contributing factors. The thermophiles have a better-packed hydrophobic core. We have also discussed how thermophiles, although increasing stability through higher connectivity retains conformational flexibility, from a cliques and communities perspective.

Comparative analysis of thermophilic and mesophilic proteins using Protein Energy Networks

Background: Thermophilic proteins sustain themselves and function at higher temperatures. Despite their structural and functional similarities with their mesophilic homologues, they show enhanced stability. Various comparative studies at genomic, protein sequence and structure levels, and experimental works highlight the different factors and dominant interacting forces contributing to this increased stability. Methods: In this comparative structure based study, we have used interaction energies between amino acids, to generate structure networks called as Protein Energy Networks (PENs). These PENs are used to compute network, sub-graph, and node specific parameters. These parameters are then compared between the thermophile-mesophile homologues. Results: The results show an increased number of clusters and low energy cliques in thermophiles as the main contributing factors for their enhanced stability. Further more, we see an increase in the number of hubs in thermophiles. We also observe no community of electrostatic cliques forming in PENs. Conclusion: In this study we were able to take an energy based network approach, to identify the factors responsible for enhanced stability of thermophiles, by comparative analysis. We were able to point out that the sub-graph parameters are the prominent contributing factors. The thermophiles have a better-packed hydrophobic core. We have also discussed how thermophiles, although increasing stability through higher connectivity retains conformational flexibility, from a cliques and communities perspective.

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.

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.

Effect of network connectivity on thermal properties of As30Te70-xTlx glasses

Alternating differential scanning calorimetry (ADSC) studies were undertaken to investigate the effect of Tl addition on the thermal properties of As30Te70-xTlx ( 6 <= x <= 22 at%) glasses. These include parameters such as glass-transition temperature (T-g), changes in specific heat capacity (Delta C-p) and relaxation enthalpy (Delta H-NR) at the glass transition. It was found that T-g of the glasses decreased with the addition of Tl, which is in contrast to the dependence of T-g in As - Te glasses on the addition of Al and In. The change in heat capacity Delta C-p through the glass transition was also found to decrease with increasing Tl content. The addition of Tl to the As - Te matrix may lead to a breaking of As - Te chains and the formation of Tl+Te- AsTe2/2 dipoles. There was no significant dependence of the change of relaxation enthalpy, through the glass transition, with composition.

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.

Functional Identification of Regulatory Elements within the Promoter Region of Platelet-Derived Growth Factor 2

Human platelet-derived growth factor (PDGF) is composed of two polypeptide chains, PDGF-1 and PDGF-2,the human homolog of the v-sis oncogene. Deregulation of PDGF-2 expression can confer a growth advantage to cells possessing the cognate receptor and, thus, may contribute to the malignant phenotype. We investigated the regulation of PDGF-2 mRNA expression during megakaryocytic differentiation of K562 cells. Induction by 12-O-tetradecanoylphorbol-13-acetate (TPA) led to a greater than 200-fold increase in PDGF-2 transcript levels in these cells. Induction was dependent on protein synthesis and was not enhanced by cycloheximide exposure.In our initial investigation of the PDGF-2 promoter, a minimal promoter region, which included sequences extending only 42 base pairs upstream of the TATA signal, was found to be as efficient as 4 kilobase pairs upstream of the TATA signal in driving expression of a reporter gene in uninduced K562 cells. We also functionally identified different regulatory sequence elements of the PDGF-2 promoter in TPA-induced K562 cells. One region acted as a transcriptional silencer, while another region was necessary for maximal activity of the promoter in megakaryoblasts. This region was shown to bind nuclear factors and was the target for trans-activation in normal and tumor cells. In one tumor cell line, which expressed high PDGF-2 mRNA levels, the presence of the positive regulatory region resulted in a 30-fold increase in promoter activity. However, the ability of the minimal PDGF-2 promoter to drive reporter gene expression in uninduced K562 cells and normal fibroblasts, which contained no detectable PDGF-2 transcripts, implies the existence of other negative control mechanisms beyond the regulation of promoter activity.