Hybrid and Rogue Kinases Encoded in the Genomes of Model Eukaryotes

The highly modular nature of protein kinases generates diverse functional roles mediated by evolutionary events such as domain recombination, insertion and deletion of domains. Usually domain architecture of a kinase is related to the subfamily to which the kinase catalytic domain belongs. However outlier kinases with unusual domain architectures serve in the expansion of the functional space of the protein kinase family. For example, Src kinases are made-up of SH2 and SH3 domains in addition to the kinase catalytic domain. A kinase which lacks these two domains but retains sequence characteristics within the kinase catalytic domain is an outlier that is likely to have modes of regulation different from classical src kinases. This study defines two types of outlier kinases: hybrids and rogues depending on the nature of domain recombination. Hybrid kinases are those where the catalytic kinase domain belongs to a kinase subfamily but the domain architecture is typical of another kinase subfamily. Rogue kinases are those with kinase catalytic domain characteristic of a kinase subfamily but the domain architecture is typical of neither that subfamily nor any other kinase subfamily. This report provides a consolidated set of such hybrid and rogue kinases gleaned from six eukaryotic genomes-S. cerevisiae, D. melanogaster, C. elegans, M. musculus, T. rubripes and H. sapiens-and discusses their functions. The presence of such kinases necessitates a revisiting of the classification scheme of the protein kinase family using full length sequences apart from classical classification using solely the sequences of kinase catalytic domains. The study of these kinases provides a good insight in engineering signalling pathways for a desired output. Lastly, identification of hybrids and rogues in pathogenic protozoa such as P. falciparum sheds light on possible strategies in host-pathogen interactions.

Typical and atypical domain combinations in human protein kinases: functions, disease causing mutations and conservation in other primates

Ser/Thr and Tyr protein kinases orchestrate many signalling pathways and hence loss in this balance leads to many disease phenotypes. Due to their high abundance, diversity and importance, efforts have been made in the past to classify kinases and annotate their functions at both gross and fine levels. These kinases are conventionally classified into subfamilies based on the sequences of catalytic domains. Usually the domain architecture of a full-length kinase is consistent with the subfamily classification made based on the sequence of kinase domain. Important contributions of modular domains to the overall function of the kinase are well known. Recently occurrence of two kinds of outlier kinases-''Hybrid'' and ``Rogue'' has been reported. These show considerable deviations in their domain architectures from the typical domain architecture known for the classical kinase subfamilies. This article provides an overview of the different subfamilies of human kinases and the role of non-kinase domains in functions and diseases. Importantly this article provides analysis of hybrid and rogue kinases encoded in the human genome and highlights their conservation in closely related primate species. These kinases are examples of elegant rewiring to bring about subtle functional differences compared to canonical variants.

Maze solving automatons for self-healing of open interconnects: Modular add-on for circuit boards

We present the circuit board integration of a self-healing mechanism to repair open faults. The electric field driven mechanism physically restores fractured interconnects in electronic circuits and has the ability to solve mazes. The repair is performed by conductive particles dispersed in an insulating fluid. We demonstrate the integration of the healing module onto printed circuit boards and the ability of maze solving. We model and perform experiments on the influence of the geometry of conductive particles as well as the terminal impedances of the route on the healing efficiency. The typical heal rate is 10 mu m/s with healed route having mean resistance of 8 k Omega across a 200 micron gap and depending on the materials and concentrations used. (C) 2015 AIP Publishing LLC.

Reduction in DNA topoisomerase I level affects growth, phenotype and nucleoid architecture of Mycobacterium smegmatis

The steady-state negative supercoiling of eubacterial genomes is maintained by the action of DNA topoisomerases. Topoisomerase distribution varies in different species of mycobacteria. While Mycobacterium tuberculosis (Mtb) contains a single type I (Topol) and a single type II (Gyrase) enzyme, Mycobacterium smegmatis (Msm) and other members harbour additional relaxases. Topol is essential for Mtb survival. However, the necessity of Topol or other relaxases in Msm has not been investigated. To recognize the importance of Topol for growth, physiology and gene expression of Msm, we have developed a conditional knock-down strain of Topol in Msm. The Topol-depleted strain exhibited extremely slow growth and drastic changes in phenotypic characteristics. The cessation of growth indicates the essential requirement of the enzyme for the organism in spite of having additional DNA relaxation enzymes in the cell. Notably, the imbalance in Topol level led to the altered expression of topology modulatory proteins, resulting in a diffused nucleoid architecture. Proteomic and transcript analysis of the mutant indicated reduced expression of the genes involved in central metabolic pathways and core DNA transaction processes. RNA polymerase (RNAP) distribution on the transcription units was affected in the Topol-depleted cells, suggesting global alteration in transcription. The study thus highlights the essential requirement of Topol in the maintenance of cellular phenotype, growth characteristics and gene expression in mycobacteria. A decrease in Topol level led to altered RNAP occupancy and impaired transcription elongation, causing severe downstream effects.

N-Terminal Disordered Domain of Saccharomyces cerevisiae Hop1 Protein Is Dispensable for DNA Binding, Bridging, and Synapsis of Double-Stranded DNA Molecules But Is Necessary for Spore Formation

The cytological architecture of the synaptonemal complex (SC), a meiosis-specific proteinaceous structure, is evolutionarily conserved among eukaryotes. However, little is known about the biochemical properties of SC components or the mechanisms underlying their roles in meiotic chromosome synapsis and recombination. Functional analysis of Saccharomyces cerevisiae Hop1, a key structural component of SC, has begun to reveal important insights into its function in interhomolog recombination. Previously, we showed that Hop1 is a structure-specific DNA-binding protein, exhibits higher binding affinity for the Holliday junction, and induces structural distortion at the core of the junction. Furthermore, Hop1 promotes DNA condensation and intra- and intermolecular synapsis between duplex DNA molecules. Here, we show that Hop1 possesses a modular domain organization, consisting of an intrinsically disordered N-terminal domain and a protease-resistant C-terminal domain (Hop1CTD). Furthermore, we found that Hop1CTD exhibits strong homotypic as well as heterotypic protein protein interactions, and its biochemical activities were similar to those of the full-length Hop1 protein. However, Hop1CTD failed to complement the meiotic recombination defects of the Delta hop1 strain, indicating that both N- and C-terminal domains of Hop1 are essential for meiosis and spore formation. Altogether, our findings reveal novel insights into the structure-function relationships of Hop1 and help to further our understanding of its role in meiotic chromosome synapsis and recombination.

Seismic response of reduced-scale modular block and rigid faced reinforced walls through shaking table tests

This paper focuses on understanding the seismic response of geosynthetic reinforced retaining walls through shaking table tests on models of modular block and rigid faced reinforced retaining walls. Reduced-scale models of retaining walls reinforced with geogrid layers were constructed in a laminar box mounted on a uniaxial shaking table and subjected to various levels of sinusoidal base shaking. Models were instrumented with ultrasonic displacement sensors, earth pressure sensors and accelerometers. Effects of backfill density, number of reinforcement layers and reinforcement type on the performance of rigid faced and modular block walls were studied through different series of model tests. Performances of the walls were assessed in terms of face deformations, crest settlement and acceleration amplification at different elevations and compared. Modular block walls performed better than the rigid faced walls for the same level of base shaking because of the additional support derived by stacking the blocks with an offset. Type and quantity of reinforcement has significant effect on the seismic performance of both the types of walls. Displacements are more sensitive to relative density of the backfill and decrease with increasing relative density, the effect being more pronounced in case of unreinforced walls compared to the reinforced ones. Acceleration amplifications are not affected by the wall facing and inclusion of reinforcement. (C) 2015 Elsevier Ltd. All rights reserved.

L-infinity norms of holomorphic modular forms in the case of compact quotient

We prove a sub-convex estimate for the sup-norm of L-2-normalized holomorphic modular forms of weight k on the upper half plane, with respect to the unit group of a quaternion division algebra over Q. More precisely we show that when the L-2 norm of an eigenfunction f is one, parallel to f parallel to(infinity) <<(epsilon) k(1/2-1/33+epsilon) for any epsilon > 0 and for all k sufficiently large.

Novel architecture for anomalous strengthening of a particulate filled polymer matrix composite

We propose an architecture for dramatically enhancing the stress bearing and energy absorption capacities of a polymer based composite. Different weight fractions of iron oxide nano-particles (NPs) are mixed in a poly(dimethylesiloxane) (PDMS) matrix either uniformly or into several vertically aligned cylindrical pillars. These composites are compressed up to a strain of 60% at a strain rate of 0.01 s(-1) following which they are fully unloaded at the same rate. Load bearing and energy absorption capacities of the composite with uniform distribution of NPs increase by similar to 50% upon addition of 5 wt% of NPs; however, these properties monotonically decrease with further addition of NPs so much so that the load bearing capacity of the composite becomes 1/6th of PDMS upon addition of 20 wt% of NPs. On the contrary, stress at a strain of 60% and energy absorption capacity of the composites with pillar configuration monotonically increase with the weight fraction of NPs in the pillars wherein the load bearing capacity becomes 1.5 times of PDMS when the pillars consisted of 20 wt% of NPs. In situ mechanical testing of composites with pillars reveals outward bending of the pillars wherein the pillars and the PDMS in between two pillars, located along a radius, are significantly compressed. Reasoning based on effects of compressive hydrostatic stress and shape of fillers is developed to explain the observed anomalous strengthening of the composite with pillar architecture.

A Pd-24 Pregnant Molecular Nanoball: Self-Templated Stellation by Precise Mapping of Coordination Sites

We found that Pd(II) ion (M) and the smallest 120 bidentate donor pyrimidine (L-a) self-assemble into a mononuclear M(L-a)(4) complex (1a) instead of the expected smallest M-12(L-a)(24) molecular ball (1), presumably due to the weak coordination nature of the pyrimidine. To construct such a pyrimidine bridged nanoball, we employed a new donor tris(4-(pyrimidin-5-yl)phenyl)amine (L); which upon selective complexation with Pd(II) ions resulted in the formation of a pregnant M24L24 molecular nanoball (2) consisting of a pyrimidine-bridged Pd-12 baby-ball supported by a Pd-12 larger mother-ball. The formation of the baby-ball was not successful without the support of the mother-ball. Thus, we created an example of a self-assembly where the inner baby-ball resembling to the predicted M-12(L-a)(24) ball (1) was incarcerated by the giant outer mother-ball by means of geometrical constraints. Facile conversion of the pregnant ball 2 to a smaller M-12(L-b)(24) ball 3 with dipyridyl donor was achieved in a single step.

High aspect ratio, processable coordination polymer gel nanotubes based on an AIE-active LMWG with tunable emission

A new TPE based low molecular weight gelator (LMWG) which displays both AIE and MCIE phenomena in gel state has been synthesized. LMWG self-assembles to form 1D nanofibers which undergo morphology transformation to coordination polymer gel (CPG) nanotubes upon metal ion coordination. CPG shows enhanced mechanical stability along with tunable emission properties.

Structural diversities in Cu(I) and Ag(I) sulfonate coordination polymers and their anion exchange properties

Two new Cu(I) compounds, namely Cu-2(bds)(bpy)(2)]center dot 2H(2)O (1) and Cu-4(bds)(2)(azpy)(4)]center dot 6H(2)O (3) (where bds = benzene-1,3-disulfonate, bpy = 4,4'-bipyridine and azpy = 4,4'-azopyridine), and four Ag(I) compounds, namely Ag-2(bds)(bpy)(2)]center dot 2H(2)O (2), Ag-2(bds)(azpy)(2)]center dot 4H(2)O (4), Ag(bds)(1/2)(bpe)]center dot 3H(2)O (5), and Ag-4(bds)(2)(tmdp)(4)]center dot 9H(2)O (6) (where bpe = 1,2-di(4-pyridyl) ethylene and tmdp = 4,4'trimethylenedipyridine), have been synthesized, and their structures were determined and characterized by elemental analysis, IR, UV-vis and thermal studies. The structure of the compounds changed from 1D (1 and 2) to 2D (3-5) and interpenetrated 3D (6). In the case of 5, a solid-state 2 + 2] photochemical cycloaddition reaction has been performed. Compound 2 exhibits a reversible anion exchange for perchlorate and permanganate, whereas the other compounds (1, 3-6) exhibit an irreversible anion exchange behaviour for perchlorate. Catalytic studies on 2 indicate Lewis acidity.

Evidence for N-7 guanine methyl transferase activity encoded within the modular domain of RNA-dependent RNA polymerase L of a Morbillivirus

Post-transcriptional modification of viral mRNA is essential for the translation of viral proteins by cellular translation machinery. Due to the cytoplasmic replication of Paramyxoviruses, the viral-encoded RNA-dependent RNA polymerase (RdRP) is thought to possess all activities required for mRNA capping and methylation. In the present work, using partially purified recombinant RNA polymerase complex of rinderpest virus expressed in insect cells, we demonstrate the in vitro methylation of capped mRNA. Further, we show that a recombinant C-terminal fragment (1717-2183 aa) of L protein is capable of methylating capped mRNA, suggesting that the various post-transcriptional activities of the L protein are located in independently folding domains.

Conformation-selective coordination-driven self-assembly of a ditopic donor with Pd-II acceptors

Coordination-driven self-assembly of 3-(5-(pyridin-3-yl)-1H-1,2,4-triazol-3-yl)pyridine (L) was investigated with 90 degrees cis-blocked Pd(II) acceptors and tetratopic Pd(NO3)(2). Although the ligand is capable of binding in several different conformations (acting as a ditopic donor through the pyridyl nitrogens), the experimental results (including X-ray structures) showed that it adopts a particular conformation when it binds with 90 degrees cis-blocked Pd(II) acceptors (two available sites) to yield 2 + 2] self-assembled macrocycles. On the other hand, with Pd(NO3)(2) (where four available sites are present) a different conformer of the same donor was selectively bound to form a molecular cubic cage. The experimental findings were corroborated well with the density functional theory (B3LYP) calculations. The tetratopic Pd(NO3)(2) yielded a 6 + 12] self-assembled Pd6L12 molecular cube, which contains a potential void occupied by nitrate and perchlorate ions. Being a triazole based ligand, the free space inside the cage is enriched with several sp(2) hybridised nitrogen atoms with lone pairs of electrons to act as Lewis basic sites. Knoevenagel condensation reactions of several aromatic aldehydes with active methylene compounds were successfully performed in reasonably high yields in the presence of the cage.

Template-free coordination-driven self-assembly of discrete hexanuclear prismatic cages employing half-sandwich octahedral Ru-2(II) acceptors and triimidazole donors

Coordination-driven self-assembly of dinuclear half-sandwich p-cymene ruthenium(II) complexes Ru-2(mu-eta(4)-C2O4)(CH3OH)(2)(eta(6)-p-cymene)(2)](O3SCF3)(2) (1a) and Ru-2(mu-eta(4)-C6H2O4)(CH3OH)(2)(eta(6)-p-cymene)(2)](O3SCF3)(2) (1b) separately with imidazole-based tritopic donors (L-1-L-2) in methanol yielded a series of hexanuclear 3+2] trigonal prismatic cages (2-5), respectively L-1 = 1,3,5-tris(imidazole-1-yl) benzene; L-2 = 4,4',4 `'-tris(imidazole-1-yl) triphenylamine]. All the self-assembled cages 2-5 were characterized by various spectroscopic techniques (multinuclear NMR, Infra-red and ESI-MS) and their sizes, shapes were obtained through geometry optimization using molecular mechanics universal force field (MMUFF) computation. Despite the possibility due to the free rotation of donor sites of imidazole ligands, of two different atropoisomeric prismatic cages (C-3h or C-s) and polymeric product, the self-selection of single (C(3)h) conformational isomeric cages as the only product is a noteworthy observation. (C) 2015 Elsevier B.V. All rights reserved.

Efficient and practical synthesis of modular chiral beta-organochalcogeno amines, ArYCH2CH(R)NH2, and single crystal structures of (S) - MsOCH2CH(Bz)NH3+ center dot Cl- and (R)-MsOCH2CH(Ph)NH3+ center dot Cl-

Modular chiral I3-organochalcogeno amines, ArYCH2CH(R)NH2 (4a-4g) where R = Me, Bz, Ph; and ArY = PhS, BzSe and 4-MeOC6H4Te respectively have been synthesized and characterized. Compounds 4a-4g were synthesized (Method II) from chiral aminoalkyl 13-methanesulfonate hydrochlorides, MsOCH2CH(R)NH3+ center dot Cl- (2a-2c) through nucleophilic displacement of MsO- with organochalcogenolate (ArY-). In another attempt (Method I) chiral beta-organotelluro amines (4a-4c) were prepared by deprotection of chiral N-boc I3-organotelluro amides, 4-MeOC6H4TeCH2CH(R)NH-Boc (3a-3c), which in turn, 13,-,1 were made from chiral N-boc 13-methanesulfonate amides (la-lc) and ArTeNa. 1H, and FTIR spectra of all the compounds (3a-3c and 4a-4g) were characteristic. The composition of 3a-3c was determined by elemental analysis. The a]TD values of 3b-3c and 4a-4g were determined. The single crystal structures of (S)-2b and (R)-2c were determined by X-Ray diffraction studies. Both (S)-2b and (R)2c were crystallized in orthorhombic system and the Flack parameter x was found 0.08(12) and 0.00(2) respectively. The crystal of (S)-2b contain two asymmetric units with gauche (A) and staggered (B) conformations. There are NH Cl-, NH-O and CH-O intra and intermolecular secondary interactions in (S)-2b and (R)-2c resulting in supramolecular structures. (C) 2015 Elsevier By. All rights reserved.