Shared Structural Features Research Articles

Structured chemical class definitions and automated matching for chemical ontology evolution

Ontologies encode the knowledge of human experts in order to allow computers to automate common tasks in a domain. They are hierarchically organised and backed by computational logic which allows automated inferences of the implicit consequences of explicitly stated knowledge. ChEBI is a database and ontology of chemical entities of biological interest [1]. Within the ontology, chemical entities are classified based on shared structural features and also based on their roles and activities in biological systems. For example, the chemical class ‘aminopyridine’ is defined as ‘Compounds containing a pyridine skeleton substituted by one or more amine groups’, while an example of a role based class is ‘antiviral drug’, which groups together chemical entities that are used as antiviral drugs, regardless of their chemical structure. We have developed a novel semi-automated system for creating structure-based chemical class definitions. Our tool allows curators to draw and visually define shared structural features for classes of chemicals, which definitions are then used to automatically detect class membership across the full chemical database. The front end is based on an extended JChemPaint [2] and the Google Web Toolkit, and the back-end on a custom extension of the Chemistry Development Kit [3]. With this tool, it is possible to define chemical classes based on molecular skeletons, substitute groups, arbitrary parts including cycles of arbitrary length, formulae and overall properties, and these features can be combined using nested logical operators. Matching these definitions to candidate structures from the database is accomplished by means of an in-memory matching procedure, validated against the existing manually curated classification in ChEBI, allowing us to iteratively refine both the definitions of classes as well as to evolve the quality of the classification in ChEBI.

Myxobacteria: natural pharmaceutical factories

Myxobacteria are amongst the top producers of natural products. The diversity and unique structural properties of their secondary metabolites is what make these social microbes highly attractive for drug discovery. Screening of products derived from these bacteria has revealed a puzzling amount of hits against infectious and non-infectious human diseases. Preying mainly on other bacteria and fungi, why would these ancient hunters manufacture compounds beneficial for us? The answer may be the targeting of shared processes and structural features conserved throughout evolution.

Exploration of plant genomes in the FLAGdb++ environment

BackgroundIn the contexts of genomics, post-genomics and systems biology approaches, data integration presents a major concern. Databases provide crucial solutions: they store, organize and allow information to be queried, they enhance the visibility of newly produced data by comparing them with previously published results, and facilitate the exploration and development of both existing hypotheses and new ideas.ResultsThe FLAGdb++ information system was developed with the aim of using whole plant genomes as physical references in order to gather and merge available genomic data from in silico or experimental approaches. Available through a JAVA application, original interfaces and tools assist the functional study of plant genes by considering them in their specific context: chromosome, gene family, orthology group, co-expression cluster and functional network. FLAGdb++ is mainly dedicated to the exploration of large gene groups in order to decipher functional connections, to highlight shared or specific structural or functional features, and to facilitate translational tasks between plant species (Arabidopsis thaliana, Oryza sativa, Populus trichocarpa and Vitis vinifera).ConclusionCombining original data with the output of experts and graphical displays that differ from classical plant genome browsers, FLAGdb++ presents a powerful complementary tool for exploring plant genomes and exploiting structural and functional resources, without the need for computer programming knowledge. First launched in 2002, a 15th version of FLAGdb++ is now available and comprises four model plant genomes and over eight million genomic features.

Characterization of a Newly Identified Mycobacterial Tautomerase with Promiscuous Dehalogenase and Hydratase Activities Reveals a Functional Link to a Recently Diverged cis-3-Chloroacrylic Acid Dehalogenase

The enzyme cis-3-chloroacrylic acid dehalogenase (cis-CaaD) is found in a bacterial pathway that degrades a synthetic nematocide, cis-1,3-dichloropropene, introduced in the 20th century. The previously determined crystal structure of cis-CaaD and its promiscuous phenylpyruvate tautomerase (PPT) activity link this dehalogenase to the tautomerase superfamily, a group of homologous proteins that are characterized by a catalytic amino-terminal proline and a β-α-β structural fold. The low-level PPT activity of cis-CaaD, which may be a vestige of the function of its progenitor, prompted us to search the databases for a homologue of cis-CaaD that was annotated as a putative tautomerase and test both its PPT and cis-CaaD activity. We identified a mycobacterial cis-CaaD homologue (designated MsCCH2) that shares key sequence and active site features with cis-CaaD. Kinetic and 1H NMR spectroscopic studies show that MsCCH2 functions as an efficient PPT and exhibits low-level promiscuous dehalogenase activity, processing both cis- and trans-3-chloroacrylic acid. To further probe the active site of MsCCH2, the enzyme was incubated with 2-oxo-3-pentynoate (2-OP). At pH 8.5, MsCCH2 is inactivated by 2-OP due to the covalent modification of Pro-1, suggesting that Pro-1 functions as a nucleophile at pH 8.5 and attacks 2-OP in a Michael-type reaction. At pH 6.5, however, MsCCH2 exhibits hydratase activity and converts 2-OP to acetopyruvate, which implies that Pro-1 is cationic at pH 6.5 and not functioning as a nucleophile. At pH 7.5, the hydratase and inactivation reactions occur simultaneously. From these results, it can be inferred that Pro-1 of MsCCH2 has a pKa value that lies in between that of a typical tautomerase (pKa of Pro-1∼6) and that of cis-CaaD (pKa of Pro-1∼9). The shared activities and structural features, coupled with the intermediate pKa of Pro-1, suggest that MsCCH2 could be characteristic of an evolutionary intermediate along the past route for the divergence of cis-CaaD from an unknown superfamily tautomerase. This makes MsCCH2 an ideal candidate for laboratory evolution of its promiscuous dehalogenase activity, which could identify additional features necessary for a fully active cis-CaaD. Such results will provide insight into pathways that could lead to the rapid divergent evolution of an efficient cis-CaaD enzyme.

Insulin/FOXO Signaling Regulates Ovarian Prostaglandins Critical for Reproduction

Abnormalities in insulin/IGF-1 signaling are associated with infertility, but the molecular mechanisms are not well understood. Here we use liquid chromatography with electrospray ionization tandem mass spectrometry to show that the C. elegans insulin/FOXO pathway regulates the metabolism of locally acting lipid hormones called prostaglandins. C. elegans prostaglandins are synthesized without prostaglandin G/H synthase homologs, the targets of nonsteroidal anti-inflammatory drugs. Our results support the model that insulin signaling promotes the conversion of oocyte polyunsaturated fatty acids (PUFAs) into F-series prostaglandins that guide sperm to the fertilization site. Reduction in insulin signaling activates DAF-16/FOXO, which represses the transcription of germline and intestinal genes required to deliver PUFAs to oocytes in lipoprotein complexes. Nutritional and neuroendocrine cues target this mechanism to control prostaglandin metabolism and reproductive output. Prostaglandins may be conserved sperm guidance factors and widespread downstream effectors of insulin actions that influence both reproductive and nonreproductive processes.

Homologs of the small RNA SgrS are broadly distributed in enteric bacteria but have diverged in size and sequence

Sugar phosphate stress in Escherichia coli is sensed and managed by the transcriptional regulator SgrR and the small RNA (sRNA) SgrS. SgrS is a dual function RNA that performs base pairing-dependent regulation of mRNA targets and encodes a small protein, SgrT. Homologs of SgrR were analyzed for gene synteny and inter-homolog identity to identify those that are likely to be functionally analogous. These 22 SgrR homologs were used to manually locate adjacent sRNAs functionally analogous to SgrS. SgrS homologs shared little sequence identity with E. coli SgrS, but most shared several structural features. The most conserved feature of SgrS homologs was the base pairing region while the most variable feature was the sgrT-coding sequence. Analyses of predicted interactions between SgrS:ptsG mRNA pairs in different organisms revealed interesting differences in the patterns of base pairing interactions. RNA pairs with more interrupted regions of complementarity had a higher proportion of G:C base pairs than those with longer contiguous stretches of complementarity. The identification of this set of homologous sRNAs and their targets sets the stage for future studies to further elucidate the molecular requirements for regulation by SgrS.

CDNA cloning and recombinant expression of the general odorant binding protein II from Spodoptera litura

A cDNA encoding the general odorant binding protein II (GOBP II) was isolated from the antennae of Spodoptera litura (SlGOBP II, GenBank Accession No. EU086371) by homologous cloning and rapid amplification of cDNA ends (RACE). Sequencing and structural analyses revealed that the open reading frame (ORF) of SlGOBP II was 489 bp, encoding 162 amino acids with a predicted MW of 18.2 kD and pI of 5.72. SlGOPB II shared typical structural features of odorant binding proteins with other insects, including the six conservative cysteine residues. The deduced amino acid sequence of SlGOPB II shared significant identity with the GOBP II from S. frugiperda and S. exigua. RT-PCR and Northern blot analyses showed that SlGOBP II was specifically expressed in the antennae. cDNA encoding SlGOBP II was constructed into the pET-32a vector and the recombinant protein was highly expressed in Escherichia coli BL21 (DE3) after induction with IPTG. SDS electrophoresis and Western blot analysis confirmed the molecular weight of the recombinant SIGOBPII i.e, 32 kD, which has a 6xHis tag at the N-terminus. The recombinant SlGOBP II was purified by single-step Ni-NTA affinity chromatography and used to raise antiserum in rabbits. ELISA showed that the titer of antiserum was 1:12800, while Western blot analysis showed that the recombinant SlGOBP II was recognized as anti-SlGOBP II antiserum.

The Structure of the Haemophilus influenzae HMW1 Pro-piece Reveals a Structural Domain Essential for Bacterial Two-partner Secretion

In pathogenic Gram-negative bacteria, many virulence factors are secreted via the two-partner secretion pathway, which consists of an exoprotein called TpsA and a cognate outer membrane translocator called TpsB. The HMW1 and HMW2 adhesins are major virulence factors in nontypeable Haemophilus influenzae and are prototype two-partner secretion pathway exoproteins. A key step in the delivery of HMW1 and HMW2 to the bacterial surface involves targeting to the HMW1B and HMW2B outer membrane translocators by an N-terminal region called the secretion domain. Here we present the crystal structure at 1.92 A of the HMW1 pro-piece (HMW1-PP), a region that contains the HMW1 secretion domain and is cleaved and released during HMW1 secretion. Structural analysis of HMW1-PP revealed a right-handed beta-helix fold containing 12 complete parallel coils and one large extra-helical domain. Comparison of HMW1-PP and the Bordetella pertussis FHA secretion domain (Fha30) reveals limited amino acid homology but shared structural features, suggesting that diverse TpsA proteins have a common structural domain required for targeting to cognate TpsB proteins. Further comparison of HMW1-PP and Fha30 structures may provide insights into the keen specificity of TpsA-TpsB interactions.

The whys and wherefores of phosphate removal

The EMBO conference/FEBS advanced course, ‘Europhosphatases Conference 2005’, on The Biology of Phosphatases, was held in Churchill College, Cambridge University, UK, between 10 and 14 July 2005. The conference was organized by D. Alexander, J. Arino and E. Da Cruz e Silva. ![][1] “Now is not the end. It is not even the beginning of the end. But it is, perhaps, the end of the beginning”. This quotation from Sir Winston Churchill had resonance at the recent ‘Europhosphatases Conference 2005’ held at Churchill College, Cambridge. Although the identity of each of the protein phosphatase genes in the human genome is now known, the challenges of determining the enzymes' interacting partners, mechanisms of regulation, physiological substrates, biological roles and their links to disease remain substantial. The timing of the conference was particularly opportune because 2005 marked the 50th anniversary of the seminal discovery, by Edmond Fischer and Edwin Krebs, of reversible protein phosphorylation—a control mechanism now appreciated to pervade all aspects of cell physiology. In this overview of the meeting, we describe the current status of the protein phosphatase field and highlight some of the emerging themes. Unlike protein kinases, which derive from a common ancestor, protein phosphatases have evolved from distinct progenitors and therefore have no common co‐factor requirements and no shared structural features. Protein phosphatases were originally characterized as hydrolysing phosphoryl groups from proteins, but it is now understood that a limited number of protein phosphatases have the capacity to remove phosphate from either phospholipids or mRNA. Protein phosphatases can be broadly classified, on the basis of their structure, into the PPP and PPM families (Barford, 1996), which dephosphorylate phosphoserine (pSer) and phosphothreonine (pThr), and into the cysteine‐based PTPs, most of which dephosphorylate either phosphotyrosine (pTyr) exclusively or pTyr and pThr. The catalytic mechanism for the protein phosphatases involves a … [1]: /embed/graphic-1.gif

RNA-controlled polymorphism in the in vivo assembly of 180-subunit and 120-subunit virions from a single capsid protein.

Repeated, specific interactions between capsid protein (CP) subunits direct virus capsid assembly and exemplify regulated protein-protein interactions. The results presented here reveal a striking in vivo switch in CP assembly. Using cryoelectron microscopy, three-dimensional image reconstruction, and molecular modeling, we show that brome mosaic virus (BMV) CP can assemble in vivo two remarkably distinct capsids that selectively package BMV-derived RNAs in the absence of BMV RNA replication: a 180-subunit capsid indistinguishable from virions produced in natural infections and a previously unobserved BMV capsid type with 120 subunits arranged as 60 CP dimers. Each such dimer contains two CPs in distinct, nonequivalent environments, in contrast to the quasi-equivalent CP environments throughout the 180-subunit capsid. This 120-subunit capsid utilizes most of the CP interactions of the 180-subunit capsid plus nonequivalent CP-CP interactions. Thus, the CP of BMV, and perhaps other viruses, can encode CP-CP interactions that are not apparent from mature virions and may function in assembly or disassembly. Shared structural features suggest that the 120- and 180-subunit capsids share assembly steps and that a common pentamer of CP dimers may be an important assembly intermediate. The ability of a single CP to switch between distinct capsids by means of alternate interactions also implies reduced evolutionary barriers between different capsid structures. The in vivo switch between alternate BMV capsids is controlled by the RNA packaged: a natural BMV genomic RNA was packaged in 180-subunit capsids, whereas an engineered mRNA containing only the BMV CP gene was packaged in 120-subunit capsids. RNA features can thus direct the assembly of a ribonucleoprotein complex between alternate structural pathways.

Molecular phylogenies based on ribosomal protein L11, L1, L10, and L12 sequences

Available sequences that correspond to the E. coli ribosomal proteins L11, L1, L10, and L12 from eubacteria, archaebacteria, and eukaryotes have been aligned. The alignments were analyzed qualitatively for shared structural features and for conservation of deletions or insertions. The alignments were further subjected to quantitative phylogenetic analysis, and the amino acid identity between selected pairs of sequences was calculated. In general, eubacteria, archaebacteria, and eukaryotes each form coherent and well-resolved nonoverlapping phylogenetic domains. The degree of diversity of the four proteins between the three groups is not uniform. For L11, the eubacterial and archaebacterial proteins are very similar whereas the eukaryotic L11 is clearly less similar. In contrast, in the case of the L12 proteins and to a lesser extent the L10 proteins, the archaebacterial and eukaryotic proteins are similar whereas the eubacterial proteins are different. The eukaryotic L1 equivalent protein has yet to be identified. If the root of the universal tree is near or within the eubacterial domain, our ribosomal protein-based phylogenies indicate that archaebacteria are monophyletic. The eukaryotic lineage appears to originate either near or within the archaebacterial domain.

T cell receptor V beta gene usage in a human alloreactive response. Shared structural features among HLA-B27-specific T cell clones.

A strategy, based on using V beta family-specific oligonucleotides, was developed for specific amplification and direct sequencing of human TCR V beta genes. With this strategy, it was possible to undertake a structural analysis of TCRs from human T cell clones in specific responses. 12 HLA-B27-specific cytotoxic clones were examined. The results reveal a nonrandom use of V beta gene diversity in this alloreactive response in that: (a) the clones express a restricted number of V beta segments, including a subset of V beta families that are significantly more related to one another than to most other V beta families; (b) five of seven clones having a particular reaction pattern with HLA-B27 subtypes possess Alanine at the D-J junction; and (c) identical J beta segments are found associated in several instances with identical or highly homologous V beta gene segments. In addition, two new V beta 13 members are reported.

Shared and distinct structural features of interstitial proteoglycans from different bovine tissues revealed by electron microscopy

Large and small interstitial proteoglycans were purified from different bovine tissues, i.e. cartilage, sclera, tendon, aorta, cornea, and bone. The structure of the molecules was compared using the glycerol spraying/rotary shadowing technique for electron microscopy. Large proteoglycans from sclera and tendon have a core protein with a domain structure similar to that previously reported for cartilage proteoglycans (Paulsson, M., Mörgelin, M., Wiedemann, H., Beardmore-Gray, M., Dunham, D., Hardingham, T., Heinegård, D., Timpl, R., and Engel, J. (1987) Biochem. J. 245, 763-772). It is comprised of a pair of globules at one end of the molecule, connected by a short extended segment, followed by a long extended domain which is terminated by a third globular domain. Large aorta proteoglycans show a somewhat different structure, with only one globular domain at each end of a long extended segment. Large sclera and aorta proteoglycans form aggregates with hyaluronate and cartilage link protein in a manner similar to that of large cartilage proteoglycans. The large proteoglycans show considerable tissue variability with regard to number, length, and spacing of glycosaminoglycan side chains. The small proteoglycans reveal a small globular core protein to which one or two glycosaminoglycans are attached. Although the main structural features do not differ, proteoglycans of the S1 class have an average glycosylation close to two glycosaminoglycans/molecule, while that of the S2 class is close to one. Differences in glycosaminoglycan length were observed between tissues and between the S1 and S2 class of proteoglycan derived from a single tissue.

The spectrin membrane skeleton: emerging concepts

Spectrins are a class of multifunctional actin-binding proteins that are associated with the cortical cytoplasm of most cells. They are distinguished by a number of shared activities and structural features. In the manunalian erythrocyte, spectrin is a heterodimer composed of subunits of 240000 Mr (a) and 220000 Mr ([3). In mammalian brain and most other tissues, the subunits are 24000 Mr and 235 000 Mr (]3). Initial reports describing nonerythroid spectrins used several names, including fodrin, calspectin, TW260/240, brain calmodulin-binding protein and brain actin-binding protein. Emerging practice favors the term spectrin, prefaced by the tissue (and often species) of origin, followed by the molecular weights (in kD) of the 0t and ]3 subunits. However, the term fodrin has also gained wide acceptance as the generic non-erythroid spectrin (240/235).