Remote homology detection based on oligomer distances

MOTIVATION: Remote homology detection is among the most intensively researched problems in bioinformatics. Currently discriminative approaches, especially kernel-based methods, provide the most accurate results. However, kernel methods also show several drawbacks: in many cases prediction of new sequences is computationally expensive, often kernels lack an interpretable model for analysis of characteristic sequence features, and finally most approaches make use of so-called hyperparameters which complicate the application of methods across different datasets. RESULTS: We introduce a feature vector representation for protein sequences based on distances between short oligomers. The corresponding feature space arises from distance histograms for any possible pair of K-mers. Our distance-based approach shows important advantages in terms of computational speed while on common test data the prediction performance is highly competitive with state-of-the-art methods for protein remote homology detection. Furthermore the learnt model can easily be analyzed in terms of discriminative features and in contrast to other methods our representation does not require any tuning of kernel hyperparameters. AVAILABILITY: Normalized kernel matrices for the experimental setup can be downloaded at www.gobics.de/thomas. Matlab code for computing the kernel matrices is available upon request. CONTACT: thomas@gobics.de, peter@gobics.de.     

Effect of glycosylation on yeast invertase oligomer stability

Yeast external invertase is a glycoprotein that exists as a dimer that can associate to form tetramers, hexamers, and octamers (Chu, F., Watorek, W., and Maley, F. (1983) Arch. Biochem. Biophys. 223, 543-555; Esmon, P. C., Esmon, B. E., Schauer, I. E., Taylor, A., and Schekman, R. (1987) J. Biol. Chem., 262, 4395-4401), a process that is facilitated by the attached oligosaccharide chains. We have studied this association by high performance liquid chromatography on a gel filtration matrix, by which procedure wild-type bakers' yeast invertase gives two peaks, and invertase from a core mutant (mnn1 mnn9) of Saccharomyces cerevisiae X2180 gives three peaks. Concentration of an invertase solution by freezing drives the dimers into higher aggregates that, at 30 degrees C, re-equilibrate to a mixture of smaller forms, the composition of which depends on pH, concentration, and time. The invertase from a mutant, mnn1 mnn9 dpg1, which underglycosylates its glycoproteins and produces invertase with 4-7 oligosaccharide chains, forms oligomers of much lower stability than the mnn1 mnn9 invertase, which has 8-11 carbohydrate chains. Both of these mutants release external invertase from the periplasm into the medium during growth, but we conclude that defects in the cell wall structure may be more important in this release than an altered tendency of the invertases to aggregate. Investigation of aggregate formation by electron microscopy revealed that all invertases, including the internal nonglycosylated enzyme, form octamers under appropriate conditions.     

Simulation study of the contribution of oligomer/oligomer binding to capsid assembly kinetics

The process by which hundreds of identical capsid proteins self-assemble into icosahedral structures is complex and poorly understood. Establishing constraints on the assembly pathways is crucial to building reliable theoretical models. For example, it is currently an open question to what degree overall assembly kinetics are dominated by one or a few most efficient pathways versus the enormous number theoretically possible. The importance of this question, however, is often overlooked due to the difficulties of addressing it in either theoretical or experimental practice. We apply a computer model based on a discrete-event simulation method to evaluate the contributions of nondominant pathways to overall assembly kinetics. This is accomplished by comparing two possible assembly models: one allowing growth to proceed only by the accretion of individual assembly subunits and the other allowing the binding of sterically compatible assembly intermediates any sizes. Simulations show that the two models perform almost identically under low binding rate conditions, where growth is strongly nucleation-limited, but sharply diverge under conditions of higher association rates or coat protein concentrations. The results suggest the importance of identifying the actual binding pattern if one is to build reliable models of capsid assembly or other complex self-assembly processes.     

Vanadate oligomer interactions with myosin

'Monovanadate' containing a mixture of at least four different vanadate species and 'decavanadate' containing apparently only two vanadate species, mainly decameric species, inhibit myosin and actomyosin ATPase activities. The addition of myosin to 'monovanadate' and 'decavanadate' solutions promotes differential increases on the 51V NMR spectral linewidths of vanadate oligomers. The relative order of line broadening upon myosin addition, reflecting the interaction of the vanadate oligomers with the protein, was V10 > V4 > V1 = 1, whereas no changes were observed for monomeric vanadate species. It is concluded that decameric and tetrameric vanadate species interact quite potently with the protein and affect myosin as well actomyosin ATPase activities.     

Hormone-sensitive lipase functions as an oligomer

Hormone-sensitive lipase (HSL) is a cytosolic neutral lipase whose activity is regulated by reversible phosphorylation and which is thought to be the rate-limiting enzyme for the mobilization of FFA from adipose tissue. In the current studies the subunit structure of HSL has been explored using sucrose gradient centrifugation and in vivo and in vitro protein-protein interactions. Evidence is provided to demonstrate that HSL exists as a functional dimer composed of homologous subunits. Dimeric HSL displayed approximately 40-fold greater activity against cholesteryl ester substrate when compared with monomeric HSL without any differences in affinity for the substrate. Truncations of HSL identified the importance of the N-terminal 300 amino acids, as well as other regions, in participating in the oligomerization of HSL. These studies support the notion that the N-terminal region of HSL represents a docking domain for protein-protein interactions and provide an additional mechanism for the posttranslational control of HSL activity in the cell via oligomerization.     

Influence of oligomer chain length on the antioxidant activity of procyanidins

The antioxidant activity of catechin monomers and procyanidin (dimers to hexamers) fractions purified from cocoa was studied in two in vitro systems: liposomes and human LDL. Liposome oxidation (evaluated as formation of 2-thiobarbituric acid reactive substances) was initiated with 2,2'-azobis (2-amidinopropane) hydrochloride (AAPH), 2,2'-azobis (2,4-dimethylvaleronitrile) (AMVN), iron/ascorbate, or UV-C; LDL oxidation (evaluated as formation of conjugated dienes) was initiated with Cu(2+) or AAPH. Catechin monomers and procyanidin fractions inhibited both liposome and LDL oxidation. Monomers, dimers, and trimers fractions were the most effective antioxidants when liposome oxidation was initiated in the aqueous phase. When oxidation was initiated in the lipid domains, higher molecular weight procyanidins were the most effective. All fractions significantly inhibited Cu-mediated LDL oxidation; no significant effect of procyanidin molecular weight was observed. The hexamer fraction was the least effective with respect to preventing AAPH initiated LDL oxidation. Results reported herein give further evidence on the influence of the oligomer chain length on the antioxidant protection by procyanidins.     

Modeling the mechanics of a DNA oligomer

DNA stretching and strand separation have been studied by molecular mechanics using an oligomer which has been the subject of nanomanipulation experiments (Noy et al., Chem. Biol. 4, 519, 1997). Adiabatic mapping of conformational energy carried out as a function of stretching leads to force/extension curves in good correlation with the experimental results. Other types of deformation are also modeled and compared with the experimental results obtained on polymeric DNA. The results highlight overall similarities, but point to thermodynamic differences and also to local base sequence effects which can be expected to play an important role at the level of biologically induced structural deformations.     

Colchicine binding to an oligomer of tubulin

An oligomeric form of tubulin present in microtubule protein prepared from mammalian brain, the 36S double ring containing tau protein, is reported to bind colchicine. Colchicine binds to each individual 6S tubulin subunit in the 36S ring without apparent effect on quarternary structure. The colchicine-oligomer complex forms by colchicine binding directly to the tubulin ring; alternatively, complexes formed by colchicine with 6S tubulin subunits associate in the presence of tau protein to form the colchicine-oligomer complex.     

Alzheimer's beta-peptide oligomer formation at physiologic concentrations

When diluted from dimethyl sulfoxide or 1,1,1,3,3,3-hexafluoro-2-propanol, synthetic human Abeta(1-42) readily forms oligomeric structures at near physiologic concentrations (1-20 nM). Oligomers 40 kDa are detected in a sandwich enzyme-linked immunosorbant assay where the capture and detection antibodies recognize the same primary sequence epitope. Monomeric peptide with a single epitope does not react in this format. Abeta(1-40) peptide does not oligomerize readily under these conditions. The rate of oligomer formation has a steep linear temperature dependence but is weakly affected by ionic strength up to 0.5M NaCl or KCl. Oligomer formation is inhibited by concentrations of Tween 20 and several other detergents well below their critical micelle concentrations. Once formed, high-molecular-weight oligomers are stabilized by Tween 20. Gel permeation chromatography of an oligomer preparation formed at nanomolar concentrations indicates that the majority of the Abeta(1-42) peptide chromatographs as monomers/dimers of apparent mw approximately 10 kDa. The most abundant oligomers have apparent mobilities corresponding to 220 kDa (48-mer) and higher multiples of this without detectable concentrations of intermediate low-molecular-weight species. Very little immunoreactive peptide appears in the void volume (>1.5 MDa) of a Superose 12 column. The oligomers are stable, rechromatographing at their original position. Abeta(1-42) oligomer formation at physiologic concentrations is a reproducible process that is amenable to kinetic analysis and inhibition.     

Milled wood lignin: a linear oligomer

The degree of polymerization (DP) of softwood and hardwood milled wood lignin samples and their branching degrees were quantitatively evaluated by a novel end-group titration approach composed of QQ-HSQC, (31)P NMR, and DFRC coupled with (31)P NMR analysis techniques. The DP of lignin can be calculated when the C9 formula, the amounts of phenolic groups, pinoresinol (β-β), diphenylethane (β-1), and phenolic diphenyl (5-5') lignin subunits have been determined. Data on the degree of polymerization of lignin obtained by NMR techniques were not affected by supramolecular aggregation processes. (31)P NMR analysis coupled with DFRC and QQ-HSQC allowed a detailed evaluation of the occurrence of condensed units in lignin and showed the terminal nature of diphenyl ether and diphenyl subunits. The resulting data unequivocally show that milled wood lignin is a linear oligomer.     

Interaction of arginine oligomer with model membrane

Short oligomers of arginine (R8) have been shown to cross readily a variety of biological barriers. A hypothesis was put forward that inverted micelles form in biological membranes in the presence of arginine oligomer peptides, facilitating their transfer through the membranes. In order to define the role of peptide-lipid interaction in this mechanism, we prepared liposomes as the model membrane to study the ability of R8 inducing calcein release from liposomes, the fusion of liposomes, R8 binding to liposomes and membrane disturbing activity of the bound R8. The results show that R8 binding to liposome membrane depends on lipid compositions, negative surface charge density and interior water phase pH values of liposomes. R8 has no activity to induce the leakage of calcein from liposomes or improve liposome fusion. R8 does not permeabilize through the membrane spontaneously. These peptides delivering drugs through membranes may depend on receptors and energy.     

Lipid interactions of an actinoporin pore-forming oligomer

The actinoporins are cytolytic toxins produced by sea anemones. Upon encountering a membrane, preferably containing sphingomyelin, they oligomerize and insert their N-terminal helix into the membrane, forming a pore. Whether sphingomyelin is specifically recognized by the protein or simply induces phase coexistence in the membrane has been debated. Here, we perform multi-microsecond molecular dynamics simulations of an octamer of fragaceatoxin C, a member of the actinoporin family, in lipid bilayers containing either pure 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) or a 1:1 mixture of DOPC and palmitoyl sphingomyelin (PSM). The complex is highly stable in both environments, with only slight fraying of the inserted helices near their N-termini. Analyzing the structural parameters of the mixed membrane in the course of the simulation, we see signs of a phase transition for PSM in the inner leaflet of the bilayer. In both leaflets, cross-interactions between lipids of different type decrease over time. Surprisingly, the aromatic loop thought to be responsible for sphingomyelin recognition interacts more with DOPC than PSM by the end of the simulation. These results support the notion that the key membrane property that actinoporins recognize is lipid phase coexistence.     

The nylon oligomer biodegradation system ofFlavobacterium andPseudomonas

This review article is a compendium of the available information on the degradation of a man-made compound, 6-aminohexanoate-oligomer, inFlavobacterium andPseudomonas strains, and discusses the molecular basis for adaptation of microorganisms toward these xenobiotic compounds. Three plasmid-encoded enzymes, 6-aminohexanoate-cyclic-dimer hydrolase (EI), 6-aminohexanoate-dimer hydrolase (EII), and endo-type 6-aminohexanoate-oligomer hydrolase (EIII) are responsible for the degradation of the oligomers. Two repeated sequences, designated RS-I and RS-II, are found on plasmid pOAD2, which is involved in 6-aminohexanoate degradation inFlavobacterium. RS-I appears 5 times on the pOAD2, and all copies have the same sequences as insertion sequence IS6100. RS-II appears twice on the plasmid. RS-IIA contains the gene encoding EII, while RS-IIB contains the gene for the analogous EII' protein. Both EII and EII' are polypeptides of 392 amino acids, which differ by 46 amino acid residues. The specific activity of the EII enzyme is 200-fold higher than that of EII'. Construction of various hybrid genes demonstrated that only the combination of two amino acid residues in the EII' enzyme can enhance the activity of the EII' to the same level as that of EII enzyme.Abbreviations EI 6-aminohexanoate-cyclic-dimer hydrolase - EII 6-aminohexanoate-dimer hydrolase - EIII endo-type 6-aminohexanoate-oligomer hydrolase - F-EI EI fromFlavobacterium - F-EII EII fromFlavobacterium - P-EI EI fromPseudomonas - P-EII EII fromPseudomonas - EII' a protein having 88% homology to the EII encoded on the RS-IIB region of pOAD2 - nylA gene for the EI enzyme - nylB gene for the EII enzyme - nylC gene for the EIII enzyme - nylB' gene for the EII' protein - kb kilo-base-pairs     

Synthesis and characterization of soluble concanavalin A oligomer

Concanavalin A, (Con A, MW 26,500/monomer unit) was crosslinked with glutaraldehyde to form soluble, high-molecular-weight (larger than MW 300,000) Con A Oligomers. After filtration to remove insoluble and low-molecular-weight portions (below 300,000 daltons), the size and molecular-weight distribution were characterized by laser light scattering and gel-filtration chromatography. The molecular-size determined by laser light scattering ranged from 870 to 4070 A, while the molecular weight determined by gel chromatography ranged from 6 x 10(5) to higher than 2 x 10(6) daltons. The affinity and kinetics of Con A oligomer binding to polysaccharide (glycogen) were evaluated by precipitation test and turbidity development, respectively. The binding with glycogen was strongest at neutral pH and showed similar activity to unmodified Con A molecules. The binding constants of alpha-D-glucose and succinyl-aminophenyl alpha-D glucopyranoside-insulin to Con A oligomer were 1.0 x 10(3)M(-1) and 4.5 x 10(4)M(-1), respectively and the binding capacity of the oligomer was nearly 85% to 95% of monomeric Con A. The complexes of saccharides and soluble Con A oligomer were stable for at least 7 days. (c) 1993 Wiley & Sons, Inc.