A database and tools for 3-D protein structure comparison and alignment using the Combinatorial Extension (CE) algorithm

The database reported here is derived using the Combinatorial Extension (CE) algorithm which compares pairs of protein polypeptide chains and provides a list of structurally similar proteins along with their structure alignments. Using CE, structure-structure alignments can provide insights into biological function. When a protein of known function is shown to be structurally similar to a protein of unknown function, a relationship might be inferred; a relationship not necessarily detectable from sequence comparison alone. Establishing structure-structure relationships in this way is of great importance as we enter an era of structural genomics where there is a likelihood of an increasing number of structures with unknown functions being determined. Thus the CE database is an example of a useful tool in the annotation of protein structures of unknown function. Comparisons can be performed on the complete PDB or on a structurally representative subset of proteins. The source protein(s) can be from the PDB (updated monthly) or uploaded by the user. CE provides sequence alignments resulting from structural alignments and Cartesian coordinates for the aligned structures, which may be analyzed using the supplied Compare3D Java applet, or downloaded for further local analysis. Searches can be run from the CE web site, http://cl.sdsc.edu/ce.html, or the database and software downloaded from the site for local use.     

Investigation of spectral conversion of d(TTAGGG)4 and d(TTAGGG)13 upon potassium titration by a G-quadruplex recognizer BMVC molecule

We have introduced a G-quadruplex-binding ligand, 3,6-bis(1-methyl-4-vinylpyridinium)carbazole diiodide (BMVC), to verify the major structure of d(T₂AG₃)₄ (H24) in potassium solution and examine the structural conversion of H24 in sodium solution upon potassium titration. The studies of circular dichroism, induced circular dichroism, spectral titration and gel competition have allowed us to determine the binding mode and binding ratio of BMVC to the H24 in solution and eliminate the parallel form as the major G-quadruplex structure. Although the mixed-type form could not be eliminated as a main component, the basket and chair forms are more likely the main components of H24 in potassium solution. In addition, the circular dichroism spectra and the job plots reveal that a longer telomeric sequence d(T₂AG₃)₁₃ (H78) could form two units of G4 structure both in sodium or potassium solutions. Of particular interest is that no appreciable change on the induced circular dichroism spectra of BMVC is found during the change of the circular dichroism patterns of H24 upon potassium titration. Considering similar spectral conversion detected for H24 and a long sequence H78 together with the G4 structure stabilized by BMVC, it is therefore unlikely that the rapid spectral conversion of H24 and H78 is due to structural change between different types of the G4 structures. With reference to the circular dichroism spectra of d(GAA)₇ and d(GAAA)₅, we suggest that the spectral conversion of H24 upon potassium titration is attributed to fast ion exchange resulting in different loop base interaction and various hydrogen bonding effects.     

Metabolomics and biomarker discovery: NMR spectral data of urine and hepatotoxicity by carbon tetrachloride, acetaminophen, and d-galactosamine in rats

The primary objective of this study was to discover biomarkers which are correlated with hepatotoxicity induced by chemicals using ¹H NMR spectral data of urine. A procedure of nuclear magnetic resonance (NMR) urinalysis using pattern recognition was proposed for early screening of the hepatotoxicity of CCl₄, acetaminophen (AAP), and d-galactosamine (GalN) in rats. The hepatotoxic compounds were expected to induce necrosis in hepatocytes. This was confirmed through blood biochemistry and histopathology. CCl₄ (1 ml/kg, po) or GalN (0.8 g/kg, ip) was single administered to Sprague–Dawley (S–D) rats and urine was collected every 24 h. Animals were sacrificed 24 h or 48 h post-dosing. AAP (2 g/kg, po) was administered for 2 days and then the animals were sacrificed 24 h after the last treatment. NMR spectroscopy revealed evidently different clustering between control groups and hepatotoxicant treatment groups in global metabolic profilings as indicated by partial least square (PLS)-discrimination analysis (DA). In targeted profilings, endogenous metabolites of allantoin, citrate, taurine, 2-oxoglutarate, acetate, lactate, phenylacetyl glycine, succinate, phenylacetate, 1-methylnicotinamide, hippurate, and benzoate were selected as putative biomarkers for hepatoxicity by CCl₄, AAP, and GalN. Comparison of our rat ¹H NMR PLS-DA data with histopathological changes suggests that ¹H NMR urinalysis can be used to predict hepatotoxicity induced by CCl₄, AAP, and GalN.     

The preparation,spectral studies,and the crystal structure of dimethylbis(O-ethylxanthato)tin(IV)

Tin-119 NMR data indicate that the tin atom in (CH₃)₂Sn(S₂COC₂H₅)₂ is four co-ordinated in dichloromethane solution. However, single crystal X-ray analysis shows the tin atom to be six co-ordinated in the solid state in which the bidentate xanthate ligands display gross asymmetry in their mode of co-ordination to the tin. The crystals are molecular and there is no association between neighbouring molecules. The unit cell of Me₂Sn(exa)₂ is orthorhombic, Pnma, a = 14.165(1), b = 7.675(9), c = 13.977(2) Å with Z = 4. The structure was refined by conventional least squares methods with final R 0.041 and R_w 0.043 for 1229 unique reflections with 1 ? 2σ(I).     

Reversed micelle solvents as tools of enzyme purification and enzyme-catalyzed conversion

Reversed micelle solvents represent nanometer-sized aqueous droplets stabilized by surfactants inside the bulk organic solvents. The aqueous cores can host various hydrophilic solutes, including bioactive substances thus revealing a challenge to the biotechnology's needs of the safe media for bioseparations and bioconversions. This review discusses the structure and the properties of reversed micelle solvents in view of the parameters that can be easily operated in technology to achieve safe liquid-liquid extraction of proteins/enzymes or bioconversion of hydrophobic substrates. The paper highlights the importance of how the reversed micelle microenvironment should be arranged with respect to the preservation of the activity of the enzyme as target product or biocatalyst. The main aspects are demonstrated with own experimental results on alpha-amylase purification and lipase-catalyzed esterification using cationic reversed micelle solvents. The trials of performing continuous processes involving reversed micellar separation and reaction media are also reviewed and the current problems are addressed.     

Magnesium (II) poly(pyrazolyl)borate derivatives - Synthesis, spectral and structural studies

A series of magnesium complexes of general formula [Mg(Tp^x)₂] (Tp^x = Tp, Tp^∗, Tp^∗Cl, pzTp) and [Mg(Tp^x)X] (X = Cl, Tp^x = Tp^tBu or pz⁰Tp^p-Tol; X = acetate, Tp^x = Tp^tBu) were synthesised from magnesium chloride or acetate and M(Tp^x) (M = K, Na or Tl) in dichloromethane or alcoholic solution. These compounds are air-stable solids, sparingly soluble in most organic solvents; they have been characterized by elemental analysis, IR, ¹H and ¹³C NMR spectra and, in selected cases, also by conductivity and molecular weight measurements. Single crystal X-ray diffraction studies of [Mg(Tp)₂], [Mg(Tp*)₂] and [Mg(Tp*^Cl)₂] show unsolvated neutral bis(tripod ligand)magnesium(II) molecules with six-coordinate magnesium atoms (〈Mg-N〉 2.167(6), 2.19(2), 2.205(4) Å).     

Metabolomics, pathway regulation, and pathway discovery

Metabolomics is a data-based research strategy, the aims of which are to identify biomarker pictures of metabolic systems and metabolic perturbations and to formulate hypotheses to be tested. It involves the assay by mass spectrometry or NMR of many metabolites present in the biological system investigated. In this minireview, we outline studies in which metabolomics led to useful biomarkers of metabolic processes. We also illustrate how the discovery potential of metabolomics is enhanced by associating it with stable isotopic techniques.     

Structure alignment of membrane proteins: Accuracy of available tools and a consensus strategy

Protein structure alignment methods are used for the detection of evolutionary and functionally related positions in proteins. A wide array of different methods are available, but the choice of the best method is often not apparent to the user. Several studies have assessed the alignment accuracy and consistency of structure alignment methods, but none of these explicitly considered membrane proteins, which are important targets for drug development and have distinct structural features. Here, we compared 13 widely used pairwise structural alignment methods on a test set of homologous membrane protein structures (called HOMEP3). Each pair of structures was aligned and the corresponding sequence alignment was used to construct homology models. The model accuracy compared to the known structures was assessed using scoring functions not incorporated in the tested structural alignment methods. The analysis shows that fragment‐based approaches such as FR‐TM‐align are the most useful for aligning structures of membrane proteins. Moreover, fragment‐based approaches are more suitable for comparison of protein structures that have undergone large conformational changes. Nevertheless, no method was clearly superior to all other methods. Additionally, all methods lack a measure to rate the reliability of a position within a structure alignment. To solve both of these problems, we propose a consensus‐type approach, combining alignments from four different methods, namely FR‐TM‐align, DaliLite, MATT, and FATCAT. Agreement between the methods is used to assign confidence values to each position of the alignment. Overall, we conclude that there remains scope for the improvement of structural alignment methods for membrane proteins. Proteins 2015; 83:1720–1732. © 2015 Wiley Periodicals, Inc.     

Synthesis,reactions, spectral and magnetic studies of bimetallic alkoxides of cobalt(II) with zirconium(IV)

A bimetallic isopropoxide of cobalt(II) with the formula Co[Zr₂(OPrⁱ)₉]₂, prepared by the reaction of COCl₂ with K[Zr₂(OPrⁱ)₉] in 1:2 molar ratio, has been shown to undergo alcoholysis reactions with graded alcohols (primary, secondary and tertiary) to afford products of the types, Co[Zr₂(OR)₉]₂ (where R = Me, Et, Prⁿ, Buⁿ, Buⁱ and Bu^s) Co[Zr₂(OPrⁱ)₃(OEt)₆]₂, Co[Zr₂(OPrⁱ)₆(OBu^s)₃]₂, CO[Zr₂(OPrⁱ)₃(OBu^s)₆]₂, Co[Zr₂(OPrⁱ)₆(OBu^t)₃]² and Co[Zr₂(OPrⁱ)₃(OR)₆]₂ (where R = Am^t or Bu^t). These derivatives have been characterized by elemental analyses and molecular weight determinations. Infrared, electronic (visible) spectral and magnetic susceptibility measurements suggest a distorted octahedral geometry for these derivatives.     

Metabolomics Study of Flavonoids and Anthocyanin-Related Gene Analysis in Kiwifruit (Actinidia chinensis) and Kiwiberry (Actinidia arguta)

Plant Molecular Biology Reporter - This study investigated the flavonoid compounds in Actinidia chinensis and Actinidia arguta fruits. A total of 125 flavonoids, including 9 anthocyanins, 12...     

Contextual alignment of biological sequences (Extended abstract)

We present a model of contextual alignment of biological sequences. It is an extension of the classical alignment, in which we assume that the cost of a substitution depends on the surrounding symbols. In this model the cost of transforming one sequence into another depends on the order of editing operations. We present efficient algorithms for calculating this cost, as well as reconstructing (the representation of) all the orders of operations which yield this optimal cost. A precise characterization of the families of linear orders which can emerge this way is given.     

Preparation, spectral characterization, cytotoxic and thermal studies of platinum (IV) thiohydrazone complexes

Platinum (IV) complexes of type [Pt(L)₂Cl₂] [where, L=benzaldehyde-N,N-diphenyl-N-thiohydrazone (L¹), salicylaldehyde-N,N-diphenyl-N-thiohydrazone (L²), acetaphenone-N,N-diphenyl-N-thiohydrazone (L³) and cyclohexanone-N,N-diphenyl-N-thiohydrazone (L⁴)] have been synthesized. The thiohydrazones can exist as thione–thiol tautomer and coordinates as a bidentate N–S ligand. The ligands found to act in monobasic bidentate fashion. Analytical data reveals that metal to ligand stoichiometry is 1:2. The complexes have been characterized by elemental analysis, IR, mass, electronic, ¹H NMR spectroscopic studies, and TG/DTA study. Various kinetic and thermodynamic parameters like order of reaction (n), activation energy (E_a), apparent activation entropy (S^#) and heat of reaction (ΔH) have also been carried out for one complex. Cytotoxic study has also been carried out for one complex.     

Super pairwise alignment (SPA): an efficient approach to global alignment for homologous sequences.

Sequence analysis is the basis of bioinformatics, while sequence alignment is a fundamental task for sequence analysis. The widely used alignment algorithm, Dynamic Programming, though generating optimal alignment, takes too much time due to its high computation complexity O(N(2)). In order to reduce computation complexity without sacrificing too much accuracy, we have developed a new approach to align two homologous sequences. The new approach presented here, adopting our novel algorithm which combines the methods of probabilistic and combinatorial analysis, reduces the computation complexity to as low as O(N). The computation speed by our program is at least 15 times faster than traditional pairwise alignment algorithms without a loss of much accuracy. We hence named the algorithm Super Pairwise Alignment (SPA). The pairwise alignment execution program based on SPA and the detailed results of the aligned sequences discussed in this article are available upon request.     

Disentangling taxonomy within the Rhabditis (Pellioditis) marina (Nematoda, Rhabditidae) species complex using molecular and morhological tools

Correct taxonomy is a prerequisite for biological research, but currently it is undergoing a serious crisis, resulting in the neglect of many highly diverse groups of organisms. In nematodes, species delimitation remains problematic due to their high morphological plasticity. Evolutionary approaches using DNA sequences can potentially overcome the problems caused by morphology, but they are also affected by theoretical flaws. A holistic approach with a combination of morphological and molecular methods can therefore produce a straightforward delimitation of species. The present study investigates the taxonomic status of some highly divergent mitochondrial haplotypes in the Rhabditis ( Pellioditis ) marina species complex by using a combination of molecular and morphological tools. We used three molecular markers (COI, ITS, D2D3) and performed phylogenetic analyses. Subsequently, morphometric data from nearly all lineages were analysed with multivariate techniques. We included R. ( P. ) mediterranea and R. (R.) nidrosiensis to infer species status of the observed lineages. The results showed that highly divergent genotypic clusters were accompanied by morphological differences, and we created a graphical polytomous key for future identifications. This study indisputably demonstrates that R. ( P. ) marina and R. ( P. ) mediterranea belong to a huge species complex and that biodiversity in free-living marine nematodes may be seriously underestimated.  © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society , 2008, 152 , 1–15.     

Nickel(II) and zinc(II) dimonensinates: Single crystal X-ray structure, spectral properties and bactericidal activity

Mononuclear transition metal complexes of the polyether ionophorous antibiotic monensin (monensic acid, MonH) with nickel(II) and zinc(II) were prepared and characterized using single crystal X-ray diffraction and spectral methods. Monensin complexes crystallize as [Ni(Mon)₂(H₂O)₂]·H₂O·5MeCN (1) and [Zn(Mon)₂(H₂O)₂]·H₂O·4.5MeCN (2), respectively, in the monoclinic space group P2₁. Compounds 1 and 2 consist of two monoanionic monensic acid ligands (monensinates) bound in a bidentate coordination mode to the transition metal ion. The metal center is placed in an octahedral environment with monensin anions occupying the equatorial plane of complexes via oxygens of carboxylate and hydroxyl groups located at the both ends of ionophore molecule. The strongly folded antibiotic anions are supported by intramolecular H-bonds, most of them originating from the two aqua ligands attached to the metal(II) ions in axial positions and completing their 6-fold coordination. The bioactivity assay reveals that the presence of divalent metal ion in the monensin complexes influences the biological properties of the ligand and should be taken into account when discussing its mode of action.     

New ruthenium(II) thiolato complexes: Synthesis, reactivity, spectral, structural and DFT studies

Ruthenium complexes [Ru(mpy)₂(DMSO)₂] (1) and [Ru(mbtz)₂(DMSO)₂] (2) containing 2-mercaptopyridine (mpy) and 2-mercaptobenzothiazole (mbtz) have been synthesized. Reactivity of 1 have been examined with 2,2′-bipyridine (bipy), 1,10-phenanthroline (phen), EPh₃ (E = P, As) and 1,2-bis(diphenylphosphino)-methane (dppm). It reacted with bipy or phen in DMF to afford [Ru(mpy)₂(bipy)] (3) and [Ru(mpy)₂(phen)] (4) while, its reaction with EPh₃ or dppm in common organic solvents failed to afford products containing EPh₃ or dppm. Complexes under investigation have been characterized by elemental analyses, spectral, electrochemical studies and structures of 1-4 have been determined crystallographically. Density functional theory calculations have been performed on 1-4 and the model complex [Ru(mpy)(PMe₃)₂] (5) using exchange correlation functionals BP86. Optimized bond length and angles are in good agreement with the structural data. The Ru-N and Ru-S bond distances in [Ru(mpy)₂]-moiety of 1 are relatively shorter than 5, indicating higher stability of 1 in comparison to 5. The WBI values of Ru-N1, Ru-N2, Ru-S1 and Ru-S2 bonds indicate Ru-mpy bonding trend as 3 > 4 > 1 > 5. There is an overall charge flow in the direction L → [Ru(mpy)₂] (L = DMSO, bipy, phen and PMe₃). Due to greater ionic character and Pauli repulsive interactions for Ru-PMe₃ bond in comparison to Ru-DMSO, the DMSO ligands in 1 may not be substituted by phosphine ligands experimentally.     

Teaching (and learning from) metabolomics: the 2006 PlantMetaNet ETNA Metabolomics Research School

Under the auspices of the European Training and Networking Activity programme of the European Union, a 'Metabolic Profiling and Data Analysis' Plant Genomics and Bioinformatics Summer School was hosted in Potsdam, Germany between 20 and 29 September 2006. Sixteen early career researchers were invited from the European Union partner nations and the so-called developing nations ( Appendix ). Lectures from invited leading European researchers provided an overview of the state of the art of these fields and seeded discussion regarding major challenges for their future advancement. Hands-on experience was provided by an example experiment – that of defining the metabolic response of Arabidopsis to treatment of a commercial herbicide of defined mode of action. This experiment was performed throughout the duration of the course in order to teach the concepts underlying extraction and machine handling as well as to provide a rich data set with which the required computation and statistical skills could be illustrated. Here we review the state of the field by describing both key lectures given at and practical aspects taught at the summer school. In addition, we disclose results that were obtained using the four distinct technical platforms at the different participating institutes. While the effects of the chosen herbicide are well documented, this study looks at a broader number of metabolites than in previous investigations. This allowed, on the one hand, not only to characterise further effects of the herbicide than previously observed but also to detect molecules other than the herbicide that were obviously present in the commercial formulation. These data and the workshop in general are all discussed in the context of the teaching of metabolomics.  

  Appendix.   List of participants in the school     

20.

Metabolomics of the wild mushroom Gymnopilus imperialis (Agaricomycetes,Basidiomycota) by UHPLC-HRMS/MS analysis and molecular network     

《Fungal biology》2022,126(2):132-138

Gymnopilus consists in a widely distributed genus of mushroom-forming fungi, especially in tropical regions of the world. Literature on Gymnopilus representatives reports the presence of oligoisoprenoids, and styrylpyrones. Considering the large number of secondary metabolites that basidiomycetes might contain, dereplication tools such as GNPS (Global Natural Products Social Molecular Networking), has become important in prospecting metabolites, saving time and work on isolation and characterization of natural products. Thus, this work identified the wild mushroom Gymnopilus imperialis and dereplicated their extracts with the aid of GNPS to annotate oligoisoprenoids. It was possible to annotate 24 oligoisoprenoids from methanol, dichloromethaneand ethyl acetate extracts of G. imperialis, 4 of them from GNPS spectral library match, and 20 from prediction based on molecular network. Moreover HRMS-ESI-(+) dereplication of the acetate extract annotated bisnoryangonin and hispidin. To the best of our knowledge, this is the first report on the annotation of a series of gymnopilins analogues based on GNPS molecular network. Our findings suggest that GNPS might be an effective, rapid, and open-source device to identify compounds and predict analogues.     

Metabolomics of the wild mushroom Gymnopilus imperialis (Agaricomycetes,Basidiomycota) by UHPLC-HRMS/MS analysis and molecular network

Gymnopilus consists in a widely distributed genus of mushroom-forming fungi, especially in tropical regions of the world. Literature on Gymnopilus representatives reports the presence of oligoisoprenoids, and styrylpyrones. Considering the large number of secondary metabolites that basidiomycetes might contain, dereplication tools such as GNPS (Global Natural Products Social Molecular Networking), has become important in prospecting metabolites, saving time and work on isolation and characterization of natural products. Thus, this work identified the wild mushroom Gymnopilus imperialis and dereplicated their extracts with the aid of GNPS to annotate oligoisoprenoids. It was possible to annotate 24 oligoisoprenoids from methanol, dichloromethaneand ethyl acetate extracts of G. imperialis, 4 of them from GNPS spectral library match, and 20 from prediction based on molecular network. Moreover HRMS-ESI-(+) dereplication of the acetate extract annotated bisnoryangonin and hispidin. To the best of our knowledge, this is the first report on the annotation of a series of gymnopilins analogues based on GNPS molecular network. Our findings suggest that GNPS might be an effective, rapid, and open-source device to identify compounds and predict analogues.