TMBETADISC-RBF: Discrimination of beta-barrel membrane proteins using RBF networks and PSSM profiles

Discriminating outer membrane proteins (OMPs) from other folding types of globular and membrane proteins is an important task both for identifying OMPs from genomic sequences and for the successful prediction of their secondary and tertiary structures. We have developed a method based on radial basis function networks and position specific scoring matrix (PSSM) profiles generated by PSI-BLAST and non-redundant protein database. Our approach with PSSM profiles has correctly predicted the OMPs with a cross-validated accuracy of 96.4% in a set of 1251 proteins, which contain 206 OMPs, 667 globular proteins and 378 alpha-helical inner membrane proteins. Furthermore, we applied our method on a dataset containing 114 OMPs, 187 TMH proteins and 195 globular proteins obtained with less than 20% sequence identity and obtained the cross-validated accuracy of 95%. This accuracy of discriminating OMPs is higher than other methods in the literature and our method could be used as an effective tool for dissecting OMPs from genomic sequences. We have developed a prediction server, TMBETADISC-RBF, which is available at http://rbf.bioinfo.tw/~sachen/OMP.html.     

TMB finding pipeline: novel approach for detecting beta-barrel membrane proteins in genomic sequences

We have developed a novel approach for dissecting transmembrane beta-barrel proteins (TMBs) in genomic sequences. The features include (i) the identification of TMBs using the preference of residue pairs in globular, transmembrane helical (TMH) and TMBs, (ii) elimination of globular/TMH proteins that show sequence identity of more than 70% for the coverage of 80% residues with known structures, (iii) elimination of globular/TMH proteins that have sequence identity of more than 60% with known sequences in SWISS-PROT, and (iv) exclusion of TMH proteins using SOSUI, a prediction system for TMH proteins. Our approach picked up 7% TMBs in all the considered genomes. The comparison between the identified TMBs in E. coli genome and available experimental data demonstrated that the new approach could correctly identify all the 11 known TMBs, whose crystal structures are available. Further, it revealed the presence of 19 TMBs, homology with known structures, 60 TMBs similar to well annotated sequences, and 54 TMBs that have high sequence similarity with Escherichia coli beta-barrel proteins deposited in Transport Classification Database (TCDB). Interestingly, the present approach identified TMBs from all 15 families in TCDB. In human genome, the occurrence of TMBs varies from 0 to 3% in different chromosomes. We suggest that our approach could lead to a step forward in the advancement of structural and functional genomics.     

Current developments on beta-barrel membrane proteins: sequence and structure analysis, discrimination and prediction

beta-barrel membrane proteins perform a variety of functions, such as mediating non-specific, passive transport of ions and small molecules, selectively passing the molecules like maltose and sucrose and are involved in voltage dependent anion channels. Understanding the structural features of beta-barrel membrane proteins and detecting them in genomic sequences are challenging tasks in structural and functional genomics. In this review, with the survey of experimentally known amino acid sequences and structures, the characteristic features of amino acid residues in beta-barrel membrane proteins and novel parameters for understanding their folding and stability will be described. The development of statistical methods and machine learning techniques for discriminating beta-barrel membrane proteins from other folding types of globular and membrane proteins will be explained along with their relative importance. Further, different methods including hydrophobicity profiles, rule based approach, amino acid properties, neural networks, hidden Markov models etc. for predicting membrane spanning segments of beta-barrel membrane proteins will be discussed. In addition, the applications of discrimination techniques for detecting beta-barrel membrane proteins in genomic sequences will be outlined. In essence, this comprehensive review would provide an overall picture about beta-barrel membrane proteins starting from the construction of datasets to genome-wide applications.     

Synthesis of amorphous carbon nanoparticles and carbon encapsulated metal nanoparticles in liquid benzene by an electric plasma discharge in ultrasonic cavitation field

A newly-developed method permits an electric plasma discharge to occur with relatively low electric power in insulating organic solutions due to the presence of an ultrasonic cavitation. A stable electric plasma could be generated in an ultrasonic cavitation field containing a thousand tiny activated bubbles, in which the electric conductivity could be improved due to formed radicals and free electrons, using copper electrodes and a titanium ultrasonic horn. This method allowed us to synthesize pyrolytic amorphous carbon nanoparticles smaller than about 30 nm in diameter from benzene liquid. In addition, we synthesized TiC nanoparticles about 50-150 nm in size, and copper nanoparticles smaller than 10 nm, which were encapsulated in multilayered graphite cages. Finally, we used GC-MS and MALDI-TOF-MS to observe and analyze the polymerized compounds and the degree of polymerization of the benzene liquid after the plasma treatment.     

High-magnetic-field electromagnetophoresis of micro-particles in a capillary flow system

The electromagnetophoretic migration of micro-particles in a capillary flow system was demonstrated using a homogeneous magnetic field applied at right angles to an electric current. We utilized a high-magnetic-field of 10 T for observing this phenomenon. When the direction of the electric current was alternatively changed, polystyrene latex particles in a flowing aqueous medium migrated zigzag affected by a Lorentz force exerted on the medium. Carbon particles also migrated in the same manner with polystyrene particles. Further, we tried the electromagnetophoretic migration of biological particles, such as yeasts and human red blood cells. The migration velocity component perpendicular to the flow was proportional to both the electric current and the magnetic flux density. These results proved that the dominant force of the zigzag migration was an electromagnetophoretic buoyancy generated in the flowing medium. Moreover, it was found that the force exerted on the particles in the magnetic field of 10 T was sufficient for the desorption of particles adsorbed on the capillary wall.     

REACTION OF SINGLET OXYGEN WITH CHOLESTEROL IN LIPOSOMAL MEMBRANES. EFFECT OF MEMBRANE FLUIDITY ON THE PHOTOOXIDATION OF CHOLESTEROL

Abstract— The photosensitized oxygenation of cholesterol in liposomal membranes results in the formation of the characteristic singlet oxygen product, 3β-hydroxy-5α-cholest-6-ene-5-hydroperoxide. The yield of this product was found to be strongly temperature dependent with 6- to 7-fold increase above the transition temperature of the membrane using 1,2-dipalmitoyl- sn -glycero-3-phosphorylcholine or 1.2-dimyristoyl- sn -glycero-3-phosphorylcholine. In contrast, the formation of the radical autoxidation products of cholesterol was not significantly enhanced in these systems by higher temperatures. We conclude from the results that the oxidation of cholesterol by singlet oxygen in the artificial membranes is affected by both membrane fluidity and amount of hematoporphyrin incorporated into the membrane. The ratio of cholesterol to phospholipid which affects the morphology of membranes is a crucial factor in determining the yield of the singlet oxygen product.     

Effects of salt on the temperature and pressure responsive properties of poly(N-vinylisobutyramide) aqueous solutions

 We examined the effects of salt on the lower critical solution temperature (LCST) and lower critical solution pressure (LCSP) of aqueous solutions of poly (N-vinylisobutyramide), polyNVIBA, and compared them with those on poly(N-isopropylacrylamide), polyNIPAAm. We found that the addition of salt (such as Na₂SO₄, NaCl, or KCl) decreased the LCST of aqueous polyNVIBA from 45 °C to below 20 °C, almost linearly with the salt concentrations and dependent on the type of salt. We observed a similar concentration-dependent decrease in LCST for polyNIPAAm. When KI or NaSCN was added to each aqueous polymer solution, some smaller increases in LCST were observed at relatively low salt concentrations; higher concentrations of salt gave an almost linear decrease in LCST. As for LCSP, the addition of most types of salt lowered the transition pressure, but the effects were much more dependent on the type and the valence of the salt (especially of anion) in both polymers. Salt with divalent anion showed a larger decrease in LCSP, but those with mono valent anion showed a relatively small decrease, even showed a slight increase at lower salt concentrations in the case of polyNVIBA. Salt with I^- or SCN^- showed evident increases in LCSP up to 1 M and was maintained higher than the control even at 2 M. We discuss the interactions of the amide group in the side chains of polymers and water and their perturbation by ions. Received: 13 November 1997 Accepted: 22 January 1998     

One-step synthesis of triethynylvinylmethanes and tetraethynylmethanes by GaCl(3)-promoted diethynylation of 1,4-enynes and 1,4-diynes

The treatment of 1,4-enynes with chlorotriethylsilylacetylene at 130 degrees C in the presence of GaCl3 gave triethynylvinylmethanes by the diethynylation at the allylic methylene moiety. The addition of 2,6-di(tert-butyl)-4-methylpyridine and tert-butyldiphenylsilanol considerably improved the yields of the products by reducing the decompositions of the substrates and products. The reaction should involve the initial formation of allylgallium from the enynes and GaCl3, where GaCl3 activated hydrocarbon C-H to generate a nucleophilic organogallium intermediate. Carbometalation with chloroacetylene followed by beta-elimination then led to the ethynylated product. Triethynylvinylmethanes were obtained by the repeated regioselective ethynylation at the 3-position of the enynes. The reaction of allylsilanes with the chloroacetylene also gave diethynylvinylmethanes, in which 1,4-enynes were formed in situ by the addition-elimination of allylgallium formed from allylsilane and GaCl3. Tetraethynylmethanes were obtained by reacting 1,4-diynes with the chloroacetylene at 150 degrees C. The structure and amount of silanol can be used to control the reactivity of GaCl3.     

A note on extensions of algebraic and formal groups I

Partially supported by Grant-in-Aid for Scientific Research #62540066