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At least 19 recordsLinked to original sources
PubMed2006

Topology description for data distributions using a topology graph with divide-and-combine learning strategy.

The topologies of data distributions are very important for data description. Usually, it is not easy to find a description that can give us an intuitional understanding of the topologies for general distributions. In this paper, a novel concept, a topology graph, is proposed as a description for the principal topology of data distribution. The topology graph builds a one-to-one correspondence between the principal topology of the distribution and the topology itself: annularity features of the principal topology correspond to the loops of the graph, and the divarication features correspond to the branches of the graph. In general, the topology graph can be considered as the skeleton of the data distribution. A divide-and-combine learning strategy is developed to find the topology graphs for general data distributions. The learning strategy is focused on the constrained local description learning and automatic topology generation. Following the learning strategy, a cluster growing algorithm is developed. Experimental results on both artificial datasets and real-world applications show good performance of the proposed algorithm.

Journal Article↗
PubMed2004

A three-dimensional, noninterpenetrating metal--organic framework with the moganite topology: a simple (4(2)x6(2)x8(2))(4x6(4)x8)(2) net containing two kinds of topologically nonequivalent points.

Self assembly of Cu(2+) with the multifunctional ligand 2-(4-pyridyl)thiazole-4-carboxylic acid (Pytac) affords the neutral 3D coordination polymer [Cu(3)(Pytac)(6)](H(2)O)(14) (hereafter, SZL-1), which has the rare moganite topology. The mineral moganite has a topology that is closely related to the well-known quartz topology, but the two topologies are differentiated by the number of topologically inequivalent nodes. Whereas only one kind of node is present in quartz, two types of topologically inequivalent nodes are present in moganite. The title compound, which has three vertices in its repeat unit, has two types of topologically inequivalent nodes with the overall vertex symbol (4(2)x6(2)x8(2))(4x6(4)x8)(2) corresponding to the moganite net. Prior to this report, few metal-organic framework materials (MOFs) have been found to contain more than one type of node, and SZL-1 is the first MOF with the moganite topology.

Journal Article↗
PubMedDate not supplied

The nature of topological parameters. I. Are topological parameters 'fundamental properties'?

Topological parameters are often used descriptors in QSAR and QSPR studies. Though easily generated from an appropriate algorithm useful in developing predictive models they are not readily interpretable. Though every molecule has an intrinsic topology it is not clear whether topological parameters are 'fundamental' properties or not. The results of correlations of various properties of sets of molecules with constant topology shows that are a function of the polarizability a alone in the case of nonpolar molecules and of both dipole moment mu and polarizability alpha in the case of polar molecules. Properties studied include melting point, boiling point, critical temperature, heat of melting, heat of vaporization, solubilties of gases in various solvents, and the ratio of the Van der Waals constants (a/b). Types of molecules studied include monatomic (rare gases), diatomic, trigonal pyramidal, and tetrahedral. Our results show that these properties are successfully modeled by alpha and mu. As they are isotopological in each data set they cannot be modeled by topological parameters. It follows then that topological parameters do not have a direct cause and effect relationship with these properties and therefore are not fundamental parameters. The conclusion of Kier and Hall that they represent electron accessibility is incorrect. Topological parameters are composite parameters representing counts of the numbers of atoms, bonds, electrons, and branching.

Chemical Phenomena↗
PubMed1999

Membrane topology and cell surface targeting of microsomal epoxide hydrolase. Evidence for multiple topological orientations.

Microsomal epoxide hydrolase (mEH) is a bifunctional membrane protein that plays a central role in the metabolism of xenobiotics and in the hepatocyte uptake of bile acids. Numerous studies have established that this protein is expressed both in the endoplasmic reticulum and at the sinusoidal plasma membrane. Preliminary evidence has suggested that mEH is expressed in the endoplasmic reticulum (ER) membrane with two distinct topological orientations. To further characterize the membrane topology and targeting of this protein, an N-glycosylation site was engineered into mEH to serve as a topological probe for the elucidation of the cellular location of mEH domains. The cDNAs for mEH and this mEH derivative (mEHg) were then expressed in vitro and in COS-7 cells. Analysis of total expressed protein in these systems indicated that mEHg was largely unglycosylated, suggesting that expression in the ER was primarily of a type I orientation (Ccyt/Nexo). However, analysis, by biotin/avidin labeling procedures, of mEHg expressed at the surface of transfected COS-7 cells, showed it to be fully glycosylated, indicating that the topological form targeted to this site originally had a type II orientation (Cexo/Ncyt) in the ER. The surface expression of mEH was also confirmed by confocal fluorescence scanning microscopy. The sensitivity of mEH topology to the charge at the N-terminal domain was demonstrated by altering the net charge over a range of 0 to +3. The introduction of one positive charge led to a significant inversion in mEH topology based on glycosylation site analysis. A truncated form of mEH lacking the N-terminal hydrophobic transmembrane domain was also detected on the extracellular surface of transfected COS-7 cells, demonstrating the existence of at least one additional transmembrane segment. These results suggest that mEH may be integrated into the membrane with multiple transmembrane domains and is inserted into the ER membrane with two topological orientations, one of which is targeted to the plasma membrane where it mediates bile acid transport.

Amino Acid Sequence↗
PubMed1991

Protein topology prediction through constraint-based search and the evaluation of topological folding rules.

An algorithm for predicting protein alpha/beta-sheet topologies from secondary structure and topological folding rules (constraints) has been developed and implemented in Prolog. This algorithm (CBS1) is based on constraint satisfaction and employs forward pruned breadth-first search and rotational invariance. CBS1 showed a 37-fold increase in efficiency over an exhaustive generate and test algorithm giving the same solution for a typical sheet of five strands whose topology was predicted from secondary structure with four topological folding constraints. Prolog specifications of a range of putative protein folding rules were then used to (i) replicate published protein topology predictions and (ii) validate these rules against known protein structures of nucleotide-binding domains. This demonstrated that (i) manual techniques for topology prediction can lead to non-exhaustive search and (ii) most of these protein folding principles were violated by specific proteins. Various extensions to the algorithm are discussed.

Algorithms↗
PubMed2002

Evaluating transmembrane topology prediction methods for the effect of signal peptide in topology prediction.

Reported performance of existing transmembrane (TM) topology prediction methods were often based on evaluations which neglected the risk of signal peptides (SP) being predicted as putative TM as well. Here, we evaluated 12 selected TM topology prediction methods (TMpred, TopPred II, DAS, TMAP, MEMSAT 2, SOSUI, PRED-TMR2, TMHMM 2.0, HMMTOP 2.0, SPLIT 3.5, TM Finder, and MPEx) for the effect of SP in prediction performance considering three SP treatments, namely: "remain" (untreated), "removed first", and "removed later". The results showed that the presence of SP significantly affected the prediction performance of the 12 selected TM topology prediction methods for all three predicted attributes (the number of transmembrane segments (TMSs), the number of TMSs plus position, and the N-tail location) and for the predicted topology (combined predictions of three attributes) by causing a reduction in prediction accuracy. In particular, lower prediction accuracies were obtained if SP is left untreated (remain) while significant increases were observed if SP is removed either first or later. However, between "removed first" and "removed later" SP treatments, the difference was statistically insignificant. In addition, we found that machine learning-based prediction methods were less affected by the presence of SP than hydropathy-based methods, but still the potential risk of degrading the prediction performance is there however to a lesser degree. Thus, when performing genome-wide analysis, the SP issue should be addressed during TM topology prediction.

Algorithms↗
PubMed2002

Structure rationalization and topology prediction of two-distinct-component organic crystals: the role of volume fraction and interface topology.

We consider here small-length-scale crystal structures with two clearly different molecular components (e.g., hydrophobic and hydrophilic). Using a perspective developed by studies on large-length-scale block copolymers and liquid crystals, we focus on the crystalline interface between the two components. We examine four types of two-component crystals: aromatic ammonium carboxylates, aromatic oligo(ethylene oxides), cyclohexylammonium carboxylates, and ether-thioether compounds. Of the 111 crystal structures found in the Cambridge Structure Database (CSD), 108 adopt one of the five generic topologies found in diblock copolymers: spheres, columns, perforated layers, layers, and bicontinuous structures. As in diblock copolymers, a key factor controlling the interfacial topology is shown to be the volume ratio of the two components. When the volume fraction of one component is less than 30% of the whole, more than five-sixths of the examined crystal structures are of columnar or spherical type. For volume fractions between 40 and 50% more than three-quarters are of lamellar or bicontinuous type. We use this model to predict the topologies of small-length-scale two-component crystals. We predict the crystal topolgies of six new crystal structures: three are predicted to be columnar, and the other three, lamellar or bicontinuous. The crystal structures of these systems were then determined by single-crystal X-ray methods. Five of the structures form in topologies consistent with the predictions: three in columns and two in layers. The remaining one forms as a perforated layer instead of the predicted columnar structure. Such predictive accuracy is consistent with the statistics of the CSD investigation.

Journal Article↗
PubMed2005

Topology and phase transitions: from an exactly solvable model to a relation between topology and thermodynamics.

The elsewhere surmized topological origin of phase transitions is given here important evidence through the analytic study of an exactly solvable model for which both topology of submanifolds of configuration space and thermodynamics are worked out. The model is a mean-field one with a k-body interaction. It undergoes a second-order phase transition for k=2 and a first-order one for k >2 . This opens a perspective for the understanding of the deep origin of first and second-order phase transitions, respectively. In particular, a remarkable theoretical result consists of a mathematical characterization of first-order transitions. Moreover, we show that a "reduced" configuration space can be defined in terms of collective variables, such that the correspondence between phase transitions and topology changes becomes one-to-one, for this model. Finally, an unusual relationship is worked out between the microscopic description of a classical N -body system and its macroscopic thermodynamic behavior. This consists of a functional dependence of thermodynamic entropy upon the Morse indexes of the critical points (saddles) of the constant energy hypersurfaces of the microscopic 2N-dimensional phase space. Thus phase space (and configuration space) topology is directly related to thermodynamics.

Journal Article↗
PubMed2002

Transmembrane topology prediction methods: a re-assessment and improvement by a consensus method using a dataset of experimentally-characterized transmembrane topologies.

We selected 10 transmembrane (TM) prediction methods (KKD, TMpred, TopPred II, DAS, TMAP, MEMSAT 2, SOSUI, PRED-TMR2, TMHMM 2.0 and HMMTOP 2.0) and re-assessed its prediction performance using a reliable dataset with 122 entries of experimentally-characterized TM topologies. Then, we improved prediction performance by a consensus prediction method. Prediction performance during re-assessment and consensus prediction were based on four attributes: (i) the number of transmembrane segments (TMSs), (ii) the number of TMSs plus TMS-position, (iii) N-tail location and (iv) TM topology. We noted that hidden Markov model-based methods dominate over other methods by individual prediction performance for all four attributes. In addition, all top-performing methods generally were model-based. Among prokaryotic sequences, HMMTOP 2.0 solely topped among other methods with prediction accuracies ranging from 64% to 86% across all attributes. However, among eukaryotic sequences, prediction performance for all the attributes was relatively poor compared with prokaryotic ones. On the other hand, our results showed that our proposed consensus prediction method significantly improved prediction performance by, at least, an additional nine percentage points particularly among prokaryotic sequences for the number of TMS (84%), number of TMS and position (80%), and TM topology attributes (74%). Although our consensus prediction method improved also the prediction performance among eukaryotic sequences, the obtained accuracies for all attributes were relatively lower than that obtained by prokaryotic counterparts particularly for TM topology.

Cell Membrane↗
PubMedDate not supplied

Representation of the molecular topology of cyclical structures by means of cycle graphs. 1. Extraction of topological properties.

In this paper, a new representation model using the existing cycles in the topological structure of the molecules is proposed. Extracting all cycles of a molecule, its topological structure can be represented by means of a weighted, colored, and nondirected graph named "cycle graph", where the nodes represent the cycles in the molecule and the edges the common nodes among those cycles. In this paper, the capacity of cycle graph for the extraction of topological descriptors contributing appropriate measures of complexity, cyclicity, and symmetry of cyclical systems is presented.

Journal Article↗
PubMed2001

Topological polymer chemistry: systematic classification of nonlinear polymer topologies.

Nonlinear polymer topologies composed of cyclic and branched polymer segments are systematically classified by reference to constitutional isomerism in a series of alkanes (CnH2n+2), monocycloalkanes (CnH2n), and polycycloalkanes (CnH2n-2, CnH2n-4, etc). Thus, the total number of chain ends (termini) and of branch points (junctions) are maintained as invariant parameters, as well as the number of branches at each junction and the connectivity of junction. On the other hand, the distance between two adjacent junctions and that between the junction and terminus are taken as variant parameters. On the basis of the classification of polymer topologies, a novel synthetic strategy by an "electrostatic self-assembly and covalent fixation" technique has been proposed to construct a variety of topologically unique polymer architectures.

Journal Article↗
PubMedDate not supplied

The nature of topological parameters. II. The composition of topological parameters.

The composition of thirty topological parameters of various types including the chi, kappa and tau parameters and the Wiener indices was determined. Those derived from alkyl and substituted alkyl groups are a function of branching and steric effects; those derived from haloalkanes and haloalkenes are a function of some combination of polarizability, dipole moment, the number of halogen atoms of each type, and the ration of the number of branches to the number of atoms in the longest chain. It follows that topological parameters are actually counts of the number of atoms of each type, bonds of each type, valence, nonbonding and core electrons, branches at each position, OH and NH bonds, and nonbonding electron pairs on O and/or N atoms. These counts can be related to polarizability, dipole moment, hydrogen bonding, and steric effects, which are the true determinants of properties and biological activities. Topological parameters themselves do not have a cause and effect relationship with the quantities they are used to model. They function because: 1. They are counts of quantities that are related to the fundamental quantities that determine properties. 2. They are composite parameters which for the purpose of obtaining a predictive empirical relationship are able to represent a data set as well as pure parameters.

Chemical Phenomena↗
PubMed1995

Topology of the alpha-subunit of Na,K-ATPase based on proteolysis. Lability of the topological organization.

Topology of the alpha-subunit of Na,K-ATPase has been analyzed utilizing proteolytic digestion. Evidence is presented for a model with 10 transmembrane segments and lability of the C-terminal domain (M7-M10). Using reconstituted proteoliposomes, inside-out oriented pumps were digested with trypsin at the cytoplasmic surface. Evidence was obtained for the M7/M8 pair and cytoplasmic splits between M8 and M9 and between M9 and M10. Because an extracellular split between M9 and M10 was also observed, using right-side-out oriented renal microsomes, we propose that the M9/M10 pair either is destabilized by cytoplasmic digestion or is intrinsically mobile. Using renal microsomes, extracellular digestion of the alpha-subunit by trypsin, chymotrypsin, or an endogenous protease has been observed, after incubation at 55 or at 45 degrees C with beta-mercaptoethanol (beta-ME) and n-butanol. Both perturbations inactivate enzyme activity. Rb ions protect against inactivation and digestion. At 45 degrees C, with beta-ME and n-butanol, trypsin and chymotrypsin cut between M7 and M8 and between M9 and M10, consistent with the 10-segment model. At 55 degrees C, the topological organization is altered, the M8/M9 connecting loop is exposed at the extracellular surface, and an additional split between M8 and M9 is observed. Extracellular digestion of the alpha-subunit is associated with digestion of the beta-subunit near the first extracellular S-S bridge. Rb ions protect the beta-subunit. Exposure to proteases of extracellular domains of both subunits appears to be caused by disruption of subunit interactions.

1-Butanol↗
PubMed2005

Phospholipids as determinants of membrane protein topology. Phosphatidylethanolamine is required for the proper topological organization of the gamma-aminobutyric acid permease (GabP) of Escherichia coli.

Evidence is accumulating that the topological organization and hence function of some membrane proteins are not solely determined by the amino acid sequence of the protein but are also influenced by the lipid composition of the membrane. The gamma-aminobutyric acid (GABA) permease (GabP) of Escherichia coli has been found in this study to be affected both topologically and kinetically by membrane lipids. Using single cysteine accessibility methods with viable E. coli strains of natural lipid composition and those lacking phosphatidylethanolamine (PE), we have shown that the N-terminal hairpin of GabP is inverted relative to the membrane in PE-lacking cells, with a hinge point in transmembrane domain III. The rate of GABA transport is reduced by more than 99% in PE-lacking cells. The Michaelis constant for GABA transport is not greatly affected nor is the dependence of transport on energy. However, "transport specificity ratio" analysis demonstrated a clear transition state stability difference for GABA and nipecotic acid between the protein in PE-containing and PE-lacking cells. The patterns of observed effects are similar to those seen with the phenylalanine transporter of E. coli (Zhang, W., Bogdanov, M. Pi, J. Pittard, A. J., and Dowhan, W. (2003) J. Biol. Chem. 278, 50128-50135), also an amino acid/polyamine/organocation family member but quite distinct from those observed with lactose permease (Bogdanov, M., Heacock, P. N., and Dowhan, W. (2002) EMBO J. 21, 2107-2116), a major facilitator superfamily member. Therefore, by extending the studies of similarities and differences in lipid responses among and between family groups, we may identify elements within the proteins that facilitate lipid responsiveness.

Binding, Competitive↗
PubMed1999

Topology effect for DNA structure of cisplatin: topological transformation of cisplatin-closed circular DNA adducts by DNA topoisomerase I.

The reaction of cis-Pt(NH3)2Cl2(cis-DDP)-closed circular DNA adducts with DNA topoisomerse I(topo I) were studied by electron microscopy. We identified unique topoisomers such as a singly-linked catenane (2(1)2), trefoil (3(1), and dimetric catenane (2(1)2), etc., by analysis with electron micrographs. These unique recombination products resulted from cis-DDP-intra-twisting looped DNA adducts by DNA topo I, and the products could be explained a new mechanism based on an odd-even number rule. Our results suggest a new model on the working mechanisms for DNA topology of cis-DDP which enhances the recombination of DNA. Based on our results, we propose the topological idea that the yields of a mini closed circular DNA and pseudo trefoil DNA, etc., can be expected by reaction of cis-DDP-DNA-histone complexes with DNA topo I in the body.

Antineoplastic Agents↗
PubMed2002

DNA topology: topological transformation of DNA by reaction of cisplatin-DNA-core histone complexes with human DNA topoisomerase.

Cis-diamminedichloroplatinium(II), an active antitumor agent binds to core-histone -SV40 DNA complexes prepared by reaction of DNA with core-histone, and alters the fiber-like structure into the loosened structure. In order to model the cisplatin-modified chromatin complexes in cell, the complexes were reacted with human DNA topo II. We found the generations of unique topologically isomers such as trefoil knot (and catenane) and pseudo catenane (and pseudo knot) by reaction of cis-DDP--linearDNA--core-histone complexes with DNA topo I. The results are discussed in relation with a possible recombinational role of topo II (or topo I) on the reaction with cis-DDP--DNA--core-histone complexes.

Cisplatin↗