Discontinuous Domain Research Articles

ThreaDom: extracting protein domain boundary information from multiple threading alignments

Motivation: Protein domains are subunits that can fold and evolve independently. Identification of domain boundary locations is often the first step in protein folding and function annotations. Most of the current methods deduce domain boundaries by sequence-based analysis, which has low accuracy. There is no efficient method for predicting discontinuous domains that consist of segments from separated sequence regions. As template-based methods are most efficient for protein 3D structure modeling, combining multiple threading alignment information should increase the accuracy and reliability of computational domain predictions.Result: We developed a new protein domain predictor, ThreaDom, which deduces domain boundary locations based on multiple threading alignments. The core of the method development is the derivation of a domain conservation score that combines information from template domain structures and terminal and internal alignment gaps. Tested on 630 non-redundant sequences, without using homologous templates, ThreaDom generates correct single- and multi-domain classifications in 81% of cases, where 78% have the domain linker assigned within ±20 residues. In a second test on 486 proteins with discontinuous domains, ThreaDom achieves an average precision 84% and recall 65% in domain boundary prediction. Finally, ThreaDom was examined on 56 targets from CASP8 and had a domain overlap rate 73, 87 and 85% with the target for Free Modeling, Hard multiple-domain and discontinuous domain proteins, respectively, which are significantly higher than most domain predictors in the CASP8. Similar results were achieved on the targets from the most recently CASP9 and CASP10 experiments.Availability: http://zhanglab.ccmb.med.umich.edu/ThreaDom/.Contact: zhng@umich.eduSupplementary information: Supplementary data are available at Bioinformatics online.

On the character variety of the four-holed sphere

We study the (relative) SL$(2, \mathbb C) character varieties of the four-holed sphere and the action of the mapping class group on them. We describe a domain of discontinuity for this action, and, in the case of real characters, show that this domain of discontinuity may be non-empty on the components where the relative Euler class is non-maximal.

Plasmon assisted thermal modulation in nanoparticles

Single-particle interactions hold the promise of nanometer-scale devices in areas such as data communications and storage, nanolithography, waveguides, renewable energy and therapeutics. We propose that the collective electronic properties possessed by noble metal nanoparticles may be exploited for device actuation via the unapparent mechanism of plasmon-assisted heat generation and flux. The temperature dependence of the dielectric function and the thermal transport properties of the particles play the central role in the feasibility of the thermally-actuated system, however the behavior of these thermoplasmonic processes is unclear. We experimentally and computationally analyzed modulation via thermoplasmonic processes on a test system of gold (Au) nano-islands. Modulation and energy transport in discontinuous domains exhibited quantitatively different characteristics compared to thin films. The results have implications for all surface plasmon based nano-devices where inevitable small-scale thermal processes are present.

A Hybrid Electromagnetics-Circuit Simulation Method Exploiting Discontinuous Galerkin Finite Element Time Domain Method

A hybrid electromagnetics (EM)-circuit simulation method employing the discontinuous Galerkin finite element time domain (DGFETD) method is developed to model single lumped port networks comprised of both linear and non-linear elements. The whole computational domain is split into two subsystems: one is the EM subsystem that is analyzed by DGFETD, while another is the circuit subsystem that is modeled by the Modified Nodal Analysis method to generate a circuit subsystem. The coupling between the EM and circuit subsystems is achieved through a lumped port. Due to the local properties of DGFETD operations, only small coupling matrix equation systems are involved. To handle non-linear devices, the standard Newton-Raphson method is applied to the established non-linear matrix equations. Numerical examples are presented to validate the proposed algorithm.

Identifying Distal cis-acting Gene-Regulatory Sequences by Expressing BACs Functionalized with loxP-Tn10 Transposons in Zebrafish.

Bacterial Artificial Chromosomes (BACs) are large pieces of DNA from the chromosomes of organisms propagated faithfully in bacteria as large extra-chromosomal plasmids. Expression of genes contained in BACs can be monitored after functionalizing the BAC DNA with reporter genes and other sequences that allow stable maintenance and propagation of the DNA in the new host organism. The DNA in BACs can be altered within its bacterial host in several ways. Here we discuss one such approach, using Tn10 mini-transposons, to introduce exogenous sequences into BACs for a variety of purposes. The largely random insertions of Tn10 transposons carrying lox sites have been used to position mammalian cell-selectable antibiotic resistance genes, enhancer-traps and inverted repeat ends of the vertebrate transposon Tol2 precisely at the ends of the genomic DNA insert in BACs. These modified BACs are suitable for expression in zebrafish or mouse, and have been used to functionally identify important long-range gene regulatory sequences in both species. Enhancer-trapping using BACs should prove uniquely useful in analyzing multiple discontinuous DNA domains that act in concert to regulate expression of a gene, and is not limited by genome accessibility issues of traditional enhancer-trapping methods.

A NEW 2D NON-SPURIOUS DISCONTINUOUS GALERKIN FINITE ELEMENT TIME DOMAIN (DG-FETD) METHOD FOR MAXWELL'S EQUATIONS

A new discontinuous Galerkin Finite Element Time Domain (DG-FETD) method for Maxwell's equations is developed. It can suppress spurious modes using basis functions based on polynomials with the same order of interpolation for electric fleld intensity E and magnetic ∞ux density B. Compared to FETD based on EH scheme, which requires difierent orders of interpolation polynomials for electric and magnetic fleld intensities, this method uses fewer unknowns and reduces the computation load. The discontinuous Galerkin method is employed to implement domain decomposition for the EB scheme based FETD. In addition, a well-posed time-domain perfectly matched layer (PML) is extended to the EB scheme to simulate the unbounded problem. Leap frog method is utilized for explicit time stepping. Numerical results demonstrate that the above proposed methods are efiective and e-cient for 2D time domain TMz multi-domain problems.

Using BAC transgenesis in zebrafish to identify regulatory sequences of the amyloid precursor protein gene in humans

BackgroundNon-coding DNA in and around the human Amyloid Precursor Protein (APP) gene that is central to Alzheimer’s disease (AD) shares little sequence similarity with that of appb in zebrafish. Identifying DNA domains regulating expression of the gene in such situations becomes a challenge. Taking advantage of the zebrafish system that allows rapid functional analyses of gene regulatory sequences, we previously showed that two discontinuous DNA domains in zebrafish appb are important for expression of the gene in neurons: an enhancer in intron 1 and sequences 28–31 kb upstream of the gene. Here we identify the putative transcription factor binding sites responsible for this distal cis-acting regulation, and use that information to identify a regulatory region of the human APP gene.ResultsFunctional analyses of intron 1 enhancer mutations in enhancer-trap BACs expressed as transgenes in zebrafish identified putative binding sites of two known transcription factor proteins, E4BP4/ NFIL3 and Forkhead, to be required for expression of appb. A cluster of three E4BP4 sites at −31 kb is also shown to be essential for neuron-specific expression, suggesting that the dependence of expression on upstream sequences is mediated by these E4BP4 sites. E4BP4/ NFIL3 and XFD1 sites in the intron enhancer and E4BP4/ NFIL3 sites at −31 kb specifically and efficiently bind the corresponding zebrafish proteins in vitro. These sites are statistically over-represented in both the zebrafish appb and the human APP genes, although their locations are different. Remarkably, a cluster of four E4BP4 sites in intron 4 of human APP exists in actively transcribing chromatin in a human neuroblastoma cell-line, SHSY5Y, expressing APP as shown using chromatin immunoprecipitation (ChIP) experiments. Thus although the two genes share little sequence conservation, they appear to share the same regulatory logic and are regulated by a similar set of transcription factors.ConclusionThe results suggest that the clock-regulated and immune system modulator transcription factor E4BP4/ NFIL3 likely regulates the expression of both appb in zebrafish and APP in humans. It suggests potential human APP gene regulatory pathways, not on the basis of comparing DNA primary sequences with zebrafish appb but on the model of conservation of transcription factors.

Multi-domain Spectral Immersed Interface Method for Solving Elliptic Equation with a Global Description of Discontinuous Functions

This paper presents the extension of the global description approach of a discontinuous function, which is proposed in the previous paper, to a spectral domain decomposition method. This multi-domain spectral immersed interface method(IIM) divides the whole computation domain into the smooth and discontinuous parts. Fewer points on the smooth domains are used via taking advantage of the high accuracy property of the spectral method, but more points on the discontinuous domains are employed to enhance the resolution of the calculation. Two discontinuous problems are tested to verify the present method. The results show that the domain decomposition technique can reduce the error of the spectral IIM, especially when more collocation points are placed around the discontinuity. The present method is favorable for the reason that the same level of the accuracy can be reached, in spite of the enlarged computational domain.

Anosov representations: domains of discontinuity and applications

The notion of Anosov representations has been introduced by Labourie in his study of the Hitchin component for SL(n,R). Subsequently, Anosov representations have been studied mainly for surface groups, in particular in the context of higher Teichmüller spaces, and for lattices in SO(1,n). In this article we extend the notion of Anosov representations to representations of arbitrary word hyperbolic groups and start the systematic study of their geometric properties. In particular, given an Anosov representation Γ→G we explicitly construct open subsets of compact G-spaces, on which Γ acts properly discontinuously and with compact quotient. As a consequence we show that higher Teichmüller spaces parametrize locally homogeneous geometric structures on compact manifolds. We also obtain applications regarding (non-standard) compact Clifford–Klein forms and compactifications of locally symmetric spaces of infinite volume.

Modeling Ductile Fracture Using the Discontinuous Velocity Domain Splitting Method

Discontinuous velocity domain splitting method (DVDS) is a mesh free method which focuses on the strain localization and completely neglect the bulk deformations. It considers the kinematic variational principle on a special class of virtual velocity fields to get an upper-bound of the limit load. To construct this class of virtual velocity fields, the rigid-plastic body is splinted into simple connected sub-domains and on each such sub-domain a rigid motion is associated. The discontinuous collapse flow velocity field results in localized deformations only, located at the boundary of the sub-domains. In the numerical applications of the DVDS method we introduce a numerical technique based on a level set description of the partition of the rigid-plastic body and on genetic minimization algorithms. In the case of in-plane deformation of pressure insensitive materials, the internal boundaries of the sub-domains are parts of circles or straight lines, tangent to the collapse velocity jumps. In this case, DVDS reduces to the block decomposition method, which was intensively used to get analytical upper bounds of the limit loads. When applied to the two notched tensile problem of a von Mises material, DVDS gives excellent results with a low computational cost. Furthermore, DVDS was applied to model collapse in pressure sensitive plastic materials. Illustrative examples for homogenous and heterogeneous Coulomb and Cam-Clay materials shows that DVDS gives excellent prediction of limit loads and on the collapse flow.

B Cell Repertoire Analysis Identifies New Antigenic Domains on Glycoprotein B of Human Cytomegalovirus which Are Target of Neutralizing Antibodies

Human cytomegalovirus (HCMV), a herpesvirus, is a ubiquitously distributed pathogen that causes severe disease in immunosuppressed patients and infected newborns. Efforts are underway to prepare effective subunit vaccines and therapies including antiviral antibodies. However, current vaccine efforts are hampered by the lack of information on protective immune responses against HCMV. Characterizing the B-cell response in healthy infected individuals could aid in the design of optimal vaccines and therapeutic antibodies. To address this problem, we determined, for the first time, the B-cell repertoire against glycoprotein B (gB) of HCMV in different healthy HCMV seropositive individuals in an unbiased fashion. HCMV gB represents a dominant viral antigenic determinant for induction of neutralizing antibodies during infection and is also a component in several experimental HCMV vaccines currently being tested in humans. Our findings have revealed that the vast majority (>90%) of gB-specific antibodies secreted from B-cell clones do not have virus neutralizing activity. Most neutralizing antibodies were found to bind to epitopes not located within the previously characterized antigenic domains (AD) of gB. To map the target structures of these neutralizing antibodies, we generated a 3D model of HCMV gB and used it to identify surface exposed protein domains. Two protein domains were found to be targeted by the majority of neutralizing antibodies. Domain I, located between amino acids (aa) 133–343 of gB and domain II, a discontinuous domain, built from residues 121–132 and 344–438. Analysis of a larger panel of human sera from HCMV seropositive individuals revealed positivity rates of >50% against domain I and >90% against domain II, respectively. In accordance with previous nomenclature the domains were designated AD-4 (Dom II) and AD-5 (Dom I), respectively. Collectively, these data will contribute to optimal vaccine design and development of antibodies effective in passive immunization.

Discontinuous Galerkin frequency domain forward modelling for the inversion of electric permittivity in the 2D case

ABSTRACTWe have recently developed a discontinuous Galerkin frequency domain modelling algorithm for the solution of the 2D transverse magnetic Maxwell equations. This method is formulated on an unstructured triangular discretization of the computational domain and makes use of a high order polynomial interpolation of the electromagnetic field components within each triangular element. The discontinuous nature of the approximation naturally allows for a local definition of the interpolation order that is, in combination with a possibly non‐conforming local refinement of the mesh, a key ingredient for obtaining a flexible and accurate discretization method. Moreover, heterogeneity of the propagation media is easily dealt with by assuming element‐wise values of the electromagnetic parameters. In this paper, we propose the use of this discontinuous Galerkin frequency domain method as the forward modelling algorithm for solving the inverse problem for the electric permittivity in the 2D case. The inversion process is based on a gradient minimization technique developed by Pratt for seismological applications. Preliminary numerical results are presented for the imaging of a simplified subsurface model with the aim of assessing the performances of the proposed inversion methodology with regards to the number of frequencies, the number of recorded data and the number of sources.

Theoretical and experimental aspects of vacuum impregnation of porous media using transparent etched networks

Vacuum impregnation is a process method in which air and native solution are removed from the porous space of a given porous material and replaced by an external solution. Vacuum impregnation is divided into two steps: Firstly, the porous material is immersed in a liquid solution and exposed to subatmospheric pressure for a given time to ensure that air trapped in the porous materials will be removed; secondly, atmospheric pressure is re-established and the external solution penetrates the pore structure of the porous material. The objective of this study was to describe the hydrodynamic mechanisms involved in vacuum impregnation of porous materials as a function of capillary number and viscosity ratio. To achieve the objectives proposed in the present study, a transparent glass micromodel 7.7 cm × 7.4 cm was first constructed using the photolithographic technique. In addition, a stainless steel vacuum tank was built. The tank top was covered with a transparent reinforced glass plate. The whole system was connected to a vacuum pump, and a conventional video camera was adapted to record the experiments. Liquid saturation was determined through the image analysis process. Capillary number and viscosity ratio were determined for the drainage and imbibition processes. For the systems studied, we conclude that transport mechanisms ranged between stable displacement and capillary fingering during the vacuum step (drainage) while transport mechanisms ranged between continuous capillary and discontinuous capillary domains during the atmospheric step (imbibition). Earlier work indicated that our proposed process should be even more efficient for realistically large systems.

On discreteness of commensurators

We begin by showing that commensurators of Zariski dense subgroups of isometry groups of symmetric spaces of non-compact type are discrete provided that the limit set on the Furstenberg boundary is not invariant under the action of a (virtual) simple factor. In particular for rank one or simple Lie groups, Zariski dense subgroups with non-empty domain of discontinuity have discrete commensurators. This generalizes a Theorem of Greenberg for Kleinian groups. We then prove that for all finitely generated, Zariski dense, infinite covolume discrete subgroups of $Isom ({\mathbb{H}}^3)$, commensurators are discrete. Together these prove discreteness of commensurators for all known examples of finitely generated, Zariski dense, infinite covolume discrete subgroups of $Isom(X)$ for $X$ a symmetric space of non-compact type.

Theoretical Studies on the Interactions and Interferences of HIV-1 Glycoprotein gp120 and Its Coreceptor CCR5

The interaction between the HIV gp120 protein and coreceptor CCR5 or CXCR4 of the host cell is critical in mediating the HIV entry process. A model for the CCR5-gp120 complex has been developed. In the model, the N-terminus of CCR5 binds to three discontinuous domains of gp120, including the fourth conserved (C4) region, β19/β20 connecting loop, and V3 loop. The second extra-cellular loop (ECL2) of CCR5 also interacts with the crown part of the gp120 V3 loop. The bindings of the three CCR5 antagonists, maraviroc, aplaviroc, and vicriviroc, to the trans-membrane domain of CCR5 have been modeled. The bindings are found to affect the conformation of the ECL2 domain, which in turn drives the N-terminus of CCR5 to an altered state. Aplaviroc is more hydrophilic than maraviroc and vicriviroc, and its binding is more interfered by solvent, resulting in a quite different effect to the structure of CCR5 compared with those of the other two molecules. The above results are in accord with experimental observations and provide a structural basis for further design of CCR5 antagonists.

Structure of RavA MoxR AAA+ protein reveals the design principles of a molecular cage modulating the inducible lysine decarboxylase activity

The MoxR family of AAA+ ATPases is widespread throughout bacteria and archaea but remains poorly characterized. We recently found that the Escherichia coli MoxR protein, RavA (Regulatory ATPase variant A), tightly interacts with the inducible lysine decarboxylase, LdcI/CadA, to form a unique cage-like structure. Here, we present the X-ray structure of RavA and show that the αβα and all-α subdomains in the RavA AAA+ module are arranged as in magnesium chelatases rather than as in classical AAA+ proteins. RavA structure also contains a discontinuous triple-helical domain as well as a β-barrel-like domain forming a unique fold, which we termed the LARA domain. The LARA domain was found to mediate the interaction between RavA and LdcI. The RavA structure provides insights into how five RavA hexamers interact with two LdcI decamers to form the RavA-LdcI cage-like structure.

Yeast hexokinase isoenzyme ScHxk2: stability of a two-domain protein with discontinuous domains

The hexokinase isoenzyme 2 of Saccharomyces cerevisiae (ScHxk2) represents an archetype of a two-domain protein with the active site located in a cleft between the two domains. Binding of the substrate glucose results in a rigid body movement of the two domains leading to a cleft closure of the active site. Both domains of this enzyme are composed of discontinuous peptide sequences. This structural feature is reflected in the stability and folding of the ScHxk2 protein. Structural transitions induced by urea treatment resulted in the population of a thermodynamically stable folding intermediate, which, however, does not correspond to a molecule with one domain folded and the other unfolded. As demonstrated by different spectroscopic techniques, both domains are structurally affected by the partial denaturation. The intermediate possesses only 40% of the native secondary structural content and a substantial increase in the Stokes radius as judged by circular dichroism and dynamic light scattering analyses. One-dimensional ¹H NMR data prove that all tryptophan residues are in a non-native environment in the intermediate, indicating substantial changes in the tertiary structure. Still, the intermediate possesses quite a high stability for a transition intermediate of about ΔG = -22 kJ mol⁻¹.

A discontinuous DNA glycosylase domain in a family of enzymes that excise 5-methylcytosine

DNA cytosine methylation (5-meC) is a widespread epigenetic mark associated to gene silencing. In plants, DEMETER-LIKE (DML) proteins typified by Arabidopsis REPRESSOR OF SILENCING 1 (ROS1) initiate active DNA demethylation by catalyzing 5-meC excision. DML proteins belong to the HhH-GPD superfamily, the largest and most functionally diverse group of DNA glycosylases, but the molecular properties that underlie their capacity to specifically recognize and excise 5-meC are largely unknown. We have found that sequence similarity to HhH-GPD enzymes in DML proteins is actually distributed over two non-contiguous segments connected by a predicted disordered region. We used homology-based modeling to locate candidate residues important for ROS1 function in both segments, and tested our predictions by site-specific mutagenesis. We found that amino acids T606 and D611 are essential for ROS1 DNA glycosylase activity, whereas mutations in either of two aromatic residues (F589 and Y1028) reverse the characteristic ROS1 preference for 5-meC over T. We also found evidence suggesting that ROS1 uses Q607 to flip out 5-meC, while the contiguous N608 residue contributes to sequence-context specificity. In addition to providing novel insights into the molecular basis of 5-meC excision, our results reveal that ROS1 and its DML homologs possess a discontinuous catalytic domain that is unprecedented among known DNA glycosylases.

Analysis of permeability; solubility and diffusivity of carbon dioxide; oxygen; and nitrogen in crystalline and liquid crystalline polymers

In general, permeability and diffusivity in crystalline and liquid crystalline polymers are thought to decrease with increasing crystallinity. However, according to our statistical literature data analysis with 300 of crystalline and liquid crystalline polymers, permeability and diffusivity of carbon dioxide, oxygen, and nitrogen were not significantly affected by crystallinity at the lower crystallinity ranges. Some of them were observed with almost constant or slightly increased values of the permeability and diffusivity at the lower crystallinity range. In contrast, finally, at a higher crystallinity, gas permeability and diffusivity decreased. No increase in the solubility is observed for crystalline and liquid crystalline polymers, regardless of the crystallinity. The crystalline structure could form discontinuously in crystalline and liquid crystalline polymers at a lower crystallinity. The crystal structure gradually grew like a phase transition from the discontinuous domains with increasing crystallinity. At a higher crystallinity, the crystal structure might effectively prevent the diffusion of gas molecules because the crystal structure could be changed from discontinuous to continuous crystal domains after phase transitions. Therefore, gas permeability and diffusivity began to diminish after the phase transition of the crystal structures.

Continuum and discrete element coupling approach to analyzing seismic responses of a slope covered by deposits

Numerical analyses of earthquake effects on the deformation, stability, and load transfer of a slope covered by deposits are traditionally based on the assumption that the slope is a continuum. It would be problematic, however, to extend these approaches to the simulation of the slide, collapse and disintegration of the deposits under seismic loading. Contrary to this, a discrete element method (DEM) provides a means to consider large displacement and rotation of the non-continuum. To take the advantages of both methods of continuum and non-continuum analyses, seismic responses of a slope covered by deposits are studied by coupling a two-dimensional (2-D) finite difference method and a 2-D DEM, with the bedrock being modelled by the finite difference grids and the deposits being represented by disks. A smooth transition across the boundaries of the continuous/discontinuous domains is obtained by imposing the compatibility condition and equilibrium condition along their interfaces. In the course of computation, the same time-step value is chosen for both continuous and discontinuous domains. The free-field boundaries are adopted for lateral grids of bedrock domain to eliminate the radiation damping effect. When the static equilibrium under gravity load is obtained, dynamic calculation begins under excitation of the seismic wave input from the continuum model bottom. In this way, responses to the earthquake of a slope covered by deposits are analyzed dynamically. Combined with field monitoring data, deformation and stability of the slope are discussed. The effects of the relevant parameters of spectrum characteristic, duration, and peak acceleration of seismic waves are further investigated and explained from the simulations.