Protein Block Expert (PBE): a web-based protein structure analysis server using a structural alphabet

Encoding protein 3D structures into 1D string using short structural prototypes or structural alphabets opens a new front for structure comparison and analysis. Using the well-documented 16 motifs of Protein Blocks (PBs) as structural alphabet, we have developed a methodology to compare protein structures that are encoded as sequences of PBs by aligning them using dynamic programming which uses a substitution matrix for PBs. This methodology is implemented in the applications available in Protein Block Expert (PBE) server. PBE addresses common issues in the field of protein structure analysis such as comparison of proteins structures and identification of protein structures in structural databanks that resemble a given structure. PBE-T provides facility to transform any PDB file into sequences of PBs. PBE-ALIGNc performs comparison of two protein structures based on the alignment of their corresponding PB sequences. PBE-ALIGNm is a facility for mining SCOP database for similar structures based on the alignment of PBs. Besides, PBE provides an interface to a database (PBE-SAdb) of preprocessed PB sequences from SCOP culled at 95% and of all-against-all pairwise PB alignments at family and superfamily levels. PBE server is freely available at http://bioinformatics.univ-reunion.fr/ PBE/.

Probing Fluorine Interactions in a Polyhydroxylated Environment: Conservation of a C-F center dot center dot center dot H-C Recognition Motif in Presence of O-H center dot center dot center dot O Hydrogen Bonds

Three conformationally locked fluorinated polycyclitols have been specially crafted on a rigid trans-decalin backbone, employing a surprisingly facile pyridine-poly(hydrogen fluoride)-mediated stereospecific epoxide ring opening as the key reaction. Molecula design of the three fluorinated probes under study focused on providing an efficient platform for (a) evaluating the ability of covalently bonded fluorine, vis-a-vis the isosteric hydroxy group, to act as a H-bond acceptor and (b) examining the possibility for an organic fluorine moiety, placed suitably in a spatially invariant position, to engage an 1,3-diaxial OH functionality in a purported intramolecular O-H center dot center dot center dot F hydrogen bond. The present endeavour reveals that C(sp(3))-F center dot center dot center dot H-C(sp(3)) hydrogen bonds, though weak and lesser investigated, can indeed be observed and supramolecular recognition motifs, involving such interactions, can be conserved even in crystal structures laden with stronger O-H center dot center dot center dot O hydrogen bonds.

Conformations of three heterocyclicperhydropyrrolobenzofurans and polymeric assembly via co-operative inter-molecular C-H center dot center dot center dot O hydrogen bonds

In 1-cyclo-hexyl-6,6,8a-trimethyl-3a,6,7,8a-tetra-hydro-1H-1-benzofuro[2,3-b]pyrrole-2,4(3H,5H)-dione, C19H27NO3, (I), and the isomorphous compounds 6,6,8a-trimethyl-1-phenyl-3a,6,7,8a-tetra-hydro-1H-1-benzofuro[2,3-b]pyrrole-2,4(3H,5H)-dione, C19H21NO3, (II), and 6,6,8a-trimethyl-1-(3-pyridyl)-3a,6,7,8a-tetra-hydro-1H-1-benzofuro[2,3-b]pyrrole-2,4(3H,5H)-dione, C18H20N2O3, (III), the tetra-hydro-benzo-dihydro-furo-pyrrolidine ring systems are folded at the cis junction of the five-membered rings, giving rise to a non-planar shape of the tricyclic cores. The dihydro-furan and pyrrolidine rings in (I) are puckered and adopt an envelope conformation. The cyclo-hexene rings adopt a half-chair conformation in all the mol-ecules, while the substituent N-cyclo-hexyl ring in (I) assumes a chair form. Short intra-molecular C-HcO contacts form S(5) and S(6) motifs. The isomorphous compounds (II) and (III) are effectively isostructural, and aggregate into chains via inter-molecular C-HcO hydrogen bonds.

Conformations of three heterocyclic perhydropyrrolobenzofurans and polymeric assembly via co-operative inter-molecular C-H center dot center dot center dot O hydrogen bonds

In 1-cyclo-hexyl-6,6,8a-trimethyl-3a,6,7,8a-tetra-hydro-1H-1-benzofuro2, 3-b]pyrrole-2,4(3H,5H)-dione, C19H27NO3, (I), and the isomorphous compounds 6,6,8a-trimethyl-1-phenyl-3a,6,7,8a-tetra-hydro-1H-1-benzofuro2,3-b]p yrrole-2,4(3H,5H)-dione, C19H21NO3, (II), and 6,6,8a-trimethyl-1-(3-pyridyl)-3a,6,7,8a-tetra-hydro-1H-1-benzofuro2, 3-b]pyrrole-2,4(3H,5H)-dione, C18H20N2O3, (III), the tetra-hydro-benzo-dihydro-furo-pyrrolidine ring systems are folded at the cis junction of the five-membered rings, giving rise to a non-planar shape of the tricyclic cores. The dihydro-furan and pyrrolidine rings in (I) are puckered and adopt an envelope conformation. The cyclo-hexene rings adopt a half-chair conformation in all the mol-ecules, while the substituent N-cyclo-hexyl ring in (I) assumes a chair form. Short intra-molecular C-HcO contacts form S(5) and S(6) motifs. The isomorphous compounds (II) and (III) are effectively isostructural, and aggregate into chains via inter-molecular C-HcO hydrogen bonds.

Genome-wide analysis and experimentation of plant serine/threonine/tyrosine-specific protein kinases

Protein tyrosine phosphorylation plays an important role in cell growth, development and oncogenesis. No classical protein tyrosine kinase has hitherto been cloned from plants. Does protein tyrosine kinase exist in plants? To address this, we have performed a genomic survey of protein tyrosine kinase motifs in plants using the delineated tyrosine phosphorylation motifs from the animal system. The Arabidopsis thaliana genome encodes 57 different protein kinases that have tyrosine kinase motifs. Animal non-receptor tyrosine kinases, SRC, ABL, LYN, FES, SEK, KIN and RAS have structural relationship with putative plant tyrosine kinases. In an extended analysis, animal receptor and non-receptor kinases, Raf and Ras kinases, mixed lineage kinases and plant serine/threonine/tyrosine (STY) protein kinases, form a well-supported group sharing a common origin within the superfamily of STY kinases. We report that plants lack bona fide tyrosine kinases, which raise an intriguing possibility that tyrosine phosphorylation is carried out by dual-specificity STY protein kinases in plants. The distribution pattern of STY protein kinase families on Arabidopsis chromosomes indicates that this gene family is partly a consequence of duplication and reshuffling of the Arabidopsis genome and of the generation of tandem repeats. Genome-wide analysis is supported by the functional expression and characterization of At2g24360 and phosphoproteomics of Arabidopsis. Evidence for tyrosine phosphorylated proteins is provided by alkaline hydrolysis, anti-phosphotyrosine immunoblotting, phosphoamino acid analysis and peptide mass fingerprinting. These results report the first comprehensive survey of genome-wide and tyrosine phosphoproteome analysis of plant STY protein kinases.

Innate Immune Recognition of RNA-virus infection in human macrophages

Innate immunity and host defence are rapidly evoked by structurally invariant molecular motifs common to microbial world, called pathogen associated molecular patterns (PAMPs). In addition to PAMPs, endogenous molecules released in response to inflammation and tissue damage, danger associated molecular patterns (DAMPs), are required for eliciting the response. The most important PAMPs of viruses are viral nucleic acids, their genome or its replication intermediates, whereas the identity and characteristics of virus infection-induced DAMPs are poorly defined. PAMPs and DAMPs engage a limited set of germ-line encoded pattern recognition receptors (PRRs) in immune and non-immune cells. Membrane-bound Toll-like receptors (TLRs), cytoplasmic retinoic acid inducible gene-I (RIG-I)-like receptors (RLRs) and nucleotide-binding oligomerization domain-like receptor (NLRs) are important PRRs involved in the recognition of the molecular signatures of viral infection, such as double-stranded ribonucleic acids (dsRNAs). Engagement of PRRs results in local and systemic innate immune responses which, when activated against viruses, evoke secretion of antiviral and pro-inflammatory cytokines, and programmed cell death i.e., apoptosis of the virus-infected cell. Macrophages are the central effector cells of innate immunity. They produce significant amounts of antiviral cytokines, called interferons (IFNs), and pro-inflammatory cytokines, such as interleukin (IL)-1β and IL-18. IL-1β and IL-18 are synthesized as inactive precursors, pro-IL-1β and pro-IL-18, that are processed by caspase-1 in a cytoplasmic multiprotein complex, called the inflammasome. After processing, these cytokines are biologically active and will be secreted. The signals and secretory routes that activate inflammasomes and the secretion of IL-1β and IL-18 during virus infections are poorly characterized. The main goal of this thesis was to characterize influenza A virus-induced innate immune responses and host-virus interactions in human primary macrophages during an infection. Methodologically, various techniques of cellular and molecular biology, as well as proteomic tools combined with bioinformatics, were utilized. Overall, the thesis provides interesting insights into inflammatory and antiviral innate immune responses, and has characterized host-virus interactions during influenza A virus-infection in human primary macrophages.

Effect of follicle-stimulating hormone and its antiserum on the activity of ornithine decarboxylase in the ovary of rat and hamster

The ability of FSH to stimulate the activity of ornithine decarboxylase (ODC) in the ovary of the immature rat and cycling hamster has been examined using specific antisera to gonadotropins. The stimulatory effect of FSH on ODC activity in the ovary of the immature rat was abolished when LH antiserum was administered along with FSH, while similar administration of FSH antiserum had no effect on LH action in stimulating ODC activity, thereby demonstrating the specificity of the LH effect. During the estrus cycle of the hamster, ODC activity in the ovary could be detected only on the evening of proestrus, the maximal activity seen at 1700 h being associated with both the Graafian follicles and the rest of the ovarian tissue. Neutralization of the proestrous FSH surge had no effect on the activity of ODC in either of these tissues, while similar administration of LH antiserum at 1300 h of proestrus completely inhibited the ODC activity in both large follicles and the rest of the ovarian tissue. Thus, the surge of LH, but not of FSH, appears to be responsible for regulating the ODC activity in the ovary of the cycling hamster.

Analysis of Cl center dot center dot center dot Cl and C-H center dot center dot center dot Cl intermolecular interactions involving chlorine in substituted 2-chloroquinoline derivatives

Six crystal structures of substituted 2-chloroquinoline derivatives have been analysed to evaluate the role of Cl atom as a self recognizing unit resulting in the formation of Cl center dot center dot center dot Cl and C-H center dot center dot center dot Cl interactions to generate supramolecular assembly in the solid state. The features of Type I and Type II geometries associated with Cl center dot center dot center dot Cl interactions have been analysed to show directional preferences leading to differences in the packing motifs in these crystal structures. C-H center dot center dot center dot Cl interactions are generated exclusively in structures depicting Type II Cl center dot center dot center dot Cl interaction have been observed in these structures.

Distribution of simple repetitive (TG/CA)n and (CT/AG)n sequences in human and rodent genomes

Sixteen million nucleotide sequence of genome of various organisms have been analysed to detect and study the extent of occurrence of simple repetitive sequences. Two sequence motifs (TG/CA)n and (CT/AG)n capable of adopting unusual DNA structures, left handed Z-conformation and triple-helical conformation respectively, are found to be abundant in rodent and human genomes, but almost completely absent in bacterial genome. (TG/CA)n and (CT/AG)n sequences are present mostly in the intron or 5'/3' flanking regions of the genes. The presence of such repeat motifs in genomic sequence of higher eukaryotes has been correlated with their possible functional significance in nucleosome organization, recombination and gene expression.

The C-Terminal Domain of the MutL Homolog from Neisseria gonorrhoeae Forms an Inverted Homodimer

The mismatch repair (MMR) pathway serves to maintain the integrity of the genome by removing mispaired bases from the newly synthesized strand. In E. coli, MutS, MutL and MutH coordinate to discriminate the daughter strand through a mechanism involving lack of methylation on the new strand. This facilitates the creation of a nick by MutH in the daughter strand to initiate mismatch repair. Many bacteria and eukaryotes, including humans, do not possess a homolog of MutH. Although the exact strategy for strand discrimination in these organisms is yet to be ascertained, the required nicking endonuclease activity is resident in the C-terminal domain of MutL. This activity is dependent on the integrity of a conserved metal binding motif. Unlike their eukaryotic counterparts, MutL in bacteria like Neisseria exist in the form of a homodimer. Even though this homodimer would possess two active sites, it still acts a nicking endonuclease. Here, we present the crystal structure of the C-terminal domain (CTD) of the MutL homolog of Neisseria gonorrhoeae (NgoL) determined to a resolution of 2.4 A. The structure shows that the metal binding motif exists in a helical configuration and that four of the six conserved motifs in the MutL family, including the metal binding site, localize together to form a composite active site. NgoL-CTD exists in the form of an elongated inverted homodimer stabilized by a hydrophobic interface rich in leucines. The inverted arrangement places the two composite active sites in each subunit on opposite lateral sides of the homodimer. Such an arrangement raises the possibility that one of the active sites is occluded due to interaction of NgoL with other protein factors involved in MMR. The presentation of only one active site to substrate DNA will ensure that nicking of only one strand occurs to prevent inadvertent and deleterious double stranded cleavage.

TLR 9 Activation in Dendritic Cells Enhances Salmonella Killing and Antigen Presentation via Involvement of the Reactive Oxygen Species

Synthetic CpG containing oligodeoxynucleotide Toll like receptor-9 agonist (CpG DNA) activates innate immunity and can stimulate antigen presentation against numerous intracellular pathogens. It was observed that Salmonella Typhimurium growth can be inhibited by the CpG DNA treatment in the murine dendritic cells. This inhibitory effect was mediated by an increased reactive oxygen species production. In addition, it was noted that CpG DNA treatment of dendritic cells during Salmonella infection leads to an increased antigen presentation. Further this increased antigen presentation was dependent on the enhanced reactive oxygen species production elicited by Toll like receptor-9 activation. With the help of an exogenous antigen it was shown that Salmonella antigen could also be cross-presented in a better way by CpG induction. These data collectively indicate that CpG DNA enhance the ability of murine dendritic cells to contain the growth of virulent Salmonella through reactive oxygen species dependent killing.

The Transcriptional Regulation of Retrotransposon BARE

The purpose of this research project was to understand the steps of the retrotransposon BARE (BArley REtrotransposon) life cycle, from regulation of transcription to Virus-Like Particle (VLP) formation and ultimate integration back into the genome. Our study concentrates mainly on BARE1 transcriptional regulation because transcription is the crucial first step in the retrotransposon life cycle. The BARE element is a Class I LTR (Long Terminal Repeat) retrotransposon belonging to the Copia superfamily and was originally isolated in our research group. The LTR retrotransposons are transcribed from promoters in the LTRs and encode proteins for packaging of their transcripts, the reverse transcription of the transcripts into cDNA, and integration of the cDNA back into the genome. BARE1 is translated as a single polyprotein and cleaved into the capsid protein (GAG), integrase (IN), and reverse transcriptase-RNaseH (RT-RH) by the integral aspartic proteinase (AP). The BARE retrotransposon family comprises more than 104 copies in the barley (Hordeum vulgare) genome. The element is bound by long terminal repeats (LTRs, 1829 bp) containing promoters required for replication, signals for RNA processing, and motifs necessary for the integration of the cDNA. Members of the BARE1 subfamily are transcribed, translated, and form virus-like particles. Several basic questions concerning transcription are explored in the thesis: BARE1 transcription control, promoter choice in different barley tissues, start and termination sites for BARE transcripts, and BARE1 transcript polyadenylation (I). Polyadenylation is an important step during mRNA maturation, and determines its stability and translatability among other characteristics. Our work has found a novel way used by BARE1 to make extra GAG protein, which is critical for VLP formation. The discovery that BARE1 uses one RNA population for protein synthesis and another RNA population for making cDNA has established the most important step of the BARE1 life cycle (III). The relationship between BARE1 and BARE2 has been investigated. Besides BARE, we have examined the retrotransposon Cassandra (II), which uses a very different transcriptional mechanism and a fully parasitic life cycle. In general, this work is focused on BARE1 promoter activity, transcriptional regulation including differential promoter usage and RNA pools, extra GAG protein production and VLP formation. The results of this study give new insights into transcription regulation of LTR retrotransposons.

HELANAL: A program to characterise helix geometry in proteins,

A detailed analysis of structural and position dependent characteristic features of helices will give a better understanding of the secondary structure formation in globular proteins. Here we describe an algorithm that quantifies the geometry of helices in proteins on the basis of their C-alpha atoms alone. The Fortran program HELANAL can extract the helices from the PDB files and then characterises the overall geometry of each helix as being linear, curved or kinked, in terms of its local structural features, viz. local helical twist and rise, virtual torsion angle, local helix origins and bending angles between successive local helix axes. Even helices with large radius of curvature are unambiguously identified as being linear or curved. The program can also be used to differentiate a kinked helix and other motifs, such as helix-loop-helix or a helix-turn-helix (with a single residue linker) with the help of local bending angles. In addition to these, the program can also be used to characterise the helix start and end as well as other types of secondary structures.

Detection of a CpA methylase in an insect system: characterization and substrate specificity

A cytosine-specific DNA methyltransferase (EC 2.1.1.37) has been purified to near homogeneity from a mealybug (Planococcus lilacinus). The enzyme can methylate cytosine residues in CpG sequences as well as CpA sequences. The apparent molecular weight of the enzyme was estimated as 135,000 daltons by FPLC. The enzyme exhibits a processive mode of action and a salt dependance similar to mammalian methylases. Mealybug methylase exhibits a preference for denatured DNA substrates.

4-Azidomethyl-7-methyl-2-oxo-2H-chromene-6-sulfonyl azide

In the title compound, C11H8N6O4S, the plane of the coumarin aromatic ring is twisted by 17.2 (2)degrees with respect to the plane of the azide group bound to the methylene substituent, whereas it is twisted by 83.2 (2)degrees to the plane of the azide attached to the sulfonyl group. The crystal structure is stabilized by weak C-H center dot center dot center dot O interactions, leading to the formation of dimers with R-2(2)(12) graph-set motifs. These dimers are further linked by weak S-O center dot center dot center dot pi and pi-pi contacts centroid-centroid distance = 3.765 (2) angstrom], leading to the formation of a layered structure.