Protocols to capture the functional plasticity of protein domain superfamilies

Most proteins comprise several domains, segments that are clearly discernable in protein structure and sequence. Over the last two decades, it has become increasingly clear that domains are often also functional modules that can be duplicated and recombined in the course of evolution. This gives rise to novel protein functions. Traditionally, protein domains are grouped into homologous domain superfamilies in resources such as SCOP and CATH. This is done primarily on the basis of similarities in their three-dimensional structures. A biologically sound subdivision of the domain superfamilies into families of sequences with conserved function has so far been missing. Such families form the ideal framework to study the evolutionary and functional plasticity of individual superfamilies. In the few existing resources that aim to classify domain families, a considerable amount of manual curation is involved. Whilst immensely valuable, the latter is inherently slow and expensive. It can thus impede large-scale application. This work describes the development and application of a fully-automatic pipeline for identifying functional families within superfamilies of protein domains. This pipeline is built around a method for clustering large-scale sequence datasets in distributed computing environments. In addition, it implements two different protocols for identifying families on the basis of the clustering results: a supervised and an unsupervised protocol. These are used depending on whether or not high-quality protein function annotation data are associated with a given superfamily. The results attained for more than 1,500 domain superfamilies are discussed in both a qualitative and quantitative manner. The use of domain sequence data in conjunction with Gene Ontology protein function annotations and a set of rules and concepts to derive families is a novel approach to large-scale domain sequence classification. Importantly, the focus lies on domain, not whole-protein function

A cnidarian homologue of an insect gustatory receptor functions in developmental body patterning.

Insect gustatory and odorant receptors (GRs and ORs) form a superfamily of novel transmembrane proteins, which are expressed in chemosensory neurons that detect environmental stimuli. Here we identify homologues of GRs (Gustatory receptor-like (Grl) genes) in genomes across Protostomia, Deuterostomia and non-Bilateria. Surprisingly, two Grls in the cnidarian Nematostella vectensis, NvecGrl1 and NvecGrl2, are expressed early in development, in the blastula and gastrula, but not at later stages when a putative chemosensory organ forms. NvecGrl1 transcripts are detected around the aboral pole, considered the equivalent to the head-forming region of Bilateria. Morpholino-mediated knockdown of NvecGrl1 causes developmental patterning defects of this region, leading to animals lacking the apical sensory organ. A deuterostome Grl from the sea urchin Strongylocentrotus purpuratus displays similar patterns of developmental expression. These results reveal an early evolutionary origin of the insect chemosensory receptor family and raise the possibility that their ancestral role was in embryonic development

Gene3D: Multi-domain annotations for protein sequence and comparative genome analysis

Gene3D (http://gene3d.biochem.ucl.ac.uk) is a database of protein domain structure annotations for protein sequences. Domains are predicted using a library of profile HMMs from 2738 CATH superfamilies. Gene3D assigns domain annotations to Ensembl and UniProt sequence sets including >6000 cellular genomes and >20 million unique protein sequences. This represents an increase of 45% in the number of protein sequences since our last publication. Thanks to improvements in the underlying data and pipeline, we see large increases in the domain coverage of sequences. We have expanded this coverage by integrating Pfam and SUPERFAMILY domain annotations, and we now resolve domain overlaps to provide highly comprehensive composite multi-domain architectures. To make these data more accessible for comparative genome analyses, we have developed novel search algorithms for searching genomes to identify related multi-domain architectures. In addition to providing domain family annotations, we have now developed a pipeline for 3D homology modelling of domains in Gene3D. This has been applied to the human genome and will be rolled out to other major organisms over the next year

Chemical composition of A and F dwarf members of the Coma Berenices open cluster

Abundances of 18 chemical elements have been derived for 11 A (normal and Am) and 11 F dwarfs members of the Coma Berenices open cluster in order to set constraints on evolutionary models including transport processes (radiative and turbulent diffusion)calculated with the Montreal code. A spectral synthesis iterative procedure has been applied to derive the abundances from selected high quality lines in high resolution high signal-to-noise echelle spectra obtained with ELODIE at the Observatoire de Haute Provence. The chemical pattern found for the A and F dwarfs in Coma Berenices is reminiscent of that found in the Hyades and the UMa moving group. In graphs representing the abundances [X/H] versus the effective temperature, the A stars often display abundances much more scattered around their mean values than the F stars do. Large star-to-star variations are detected for A stars in their abundances which we interpret as evidence of transport processes competing with radiative diffusion. The F stars have solar abundances for almost all elements except for Mg, Si, V and Ba. The derived abundances patterns, [X/H] versus atomic number, for the slow rotator HD108642 (A2m) and the moderately fast rotator HD106887 (A4m) were compared to the predictions of self consistent evolutionary model codes including radiative and different amounts of turbulent diffusion. None of the models reproduces entirely the overall shape of the abundance pattern. While part of the discrepancies between derived and predicted abundances may be accounted for by non-LTE effects, the inclusion of competing processes such as rotational mixing in the radiative zones of these stars seems necessary to improve the agreement between observed and predicted abundance patterns.Comment: 25 pages, 20 figure

First Stellar Abundances in the Dwarf Irregular Galaxy Sextans A

We present the abundance analyses of three isolated A-type supergiant stars in the dwarf irregular galaxy Sextans A from high-resolution spectra the UVES spectrograph at the VLT. Detailed model atmosphere analyses have been used to determine the stellar atmospheric parameters and the elemental abundances of the stars. The mean iron group abundance was determined from these three stars to be [(FeII,CrII)/H]=-0.99+/-0.04+/-0.06. This is the first determination of the present-day iron group abundances in Sextans A. These three stars now represent the most metal-poor massive stars for which detailed abundance analyses have been carried out. The mean stellar alpha element abundance was determined from the alpha element magnesium as [alpha(MgI)/H]=-1.09+/-0.02+/-0.19. This is in excellent agreement with the nebular alpha element abundances as determined from oxygen in the H II regions. These results are consistent from star-to-star with no significant spatial variations over a length of 0.8 kpc in Sextans A. This supports the nebular abundance studies of dwarf irregular galaxies, where homogeneous oxygen abundances are found throughout, and argues against in situ enrichment. The alpha/Fe abundance ratio is [alpha(MgI)/FeII,CrII]=-0.11+/-0.02+/-0.10, which is consistent with the solar ratio. This is consistent with the results from A-supergiant analyses in other Local Group dwarf irregular galaxies but in stark contrast with the high [alpha/Fe] results from metal-poor stars in the Galaxy, and is most clearly seen from these three stars in Sextans A because of their lower metallicities. The low [alpha/Fe] ratios are consistent with the slow chemical evolution expected for dwarf galaxies from analyses of their stellar populations.Comment: 40 pages, 8 figures, accepted for publication in A

Localization length and impurity dielectric susceptibility in the critical regime of the metal-insulator transition in homogeneously doped p-type Ge

We have determined the localization length \xi and the impurity dielectric susceptibility \chi_{\rm imp} as a function of Ga acceptor concentrations (N) in nominally uncompensated ^{70}Ge:Ga just below the critical concentration (N_c) for the metal-insulator transition. Both \xi and \chi_{\rm imp} diverge at N_c according to the functions \xi\propto(1-N/N_c)^{-\nu} and \chi_{\rm imp}\propto(N_c/N-1)^{-\zeta}, respectively, with \nu=1.2\pm0.3 and \zeta=2.3\pm0.6 for 0.99N_c< N< N_c. Outside of this region (N<0.99N_c), the values of the exponents drop to \nu=0.33\pm0.03 and \zeta=0.62\pm0.05. The effect of the small amount of compensating dopants that are present in our nominally uncompensated samples, may be responsible for the change of the critical exponents at N\approx0.99N_c.Comment: RevTeX, 4 pages with 5 embedded figures, final version (minor changes

Sub-electron Charge Relaxation via 2D Hopping Conductors

We have extended Monte Carlo simulations of hopping transport in completely disordered 2D conductors to the process of external charge relaxation. In this situation, a conductor of area $L \times W$ shunts an external capacitor $C$ with initial charge $Q_i$. At low temperatures, the charge relaxation process stops at some "residual" charge value corresponding to the effective threshold of the Coulomb blockade of hopping. We have calculated the r.m.s$.$ value $Q_R$ of the residual charge for a statistical ensemble of capacitor-shunting conductors with random distribution of localized sites in space and energy and random $Q_i$, as a function of macroscopic parameters of the system. Rather unexpectedly, $Q_{R}$ has turned out to depend only on some parameter combination: $X_0 \equiv L W \nu_0 e^2/C$ for negligible Coulomb interaction and $X_{\chi} \equiv LW \kappa^2/C^{2}$ for substantial interaction. (Here $\nu_0$ is the seed density of localized states, while $\kappa$ is the dielectric constant.) For sufficiently large conductors, both functions $Q_{R}/e =F(X)$ follow the power law $F(X)=DX^{-\beta}$, but with different exponents: $\beta = 0.41 \pm 0.01$ for negligible and $\beta = 0.28 \pm 0.01$ for significant Coulomb interaction. We have been able to derive this law analytically for the former (most practical) case, and also explain the scaling (but not the exact value of the exponent) for the latter case. In conclusion, we discuss possible applications of the sub-electron charge transfer for "grounding" random background charge in single-electron devices.Comment: 12 pages, 5 figures. In addition to fixing minor typos and updating references, the discussion has been changed and expande

Electronic correlation effects and the Coulomb gap at finite temperature

We have investigated the effect of the long-range Coulomb interaction on the one-particle excitation spectrum of n-type Germanium, using tunneling spectroscopy on mechanically controllable break junctions. The tunnel conductance was measured as a function of energy and temperature. At low temperatures, the spectra reveal a minimum at zero bias voltage due to the Coulomb gap. In the temperature range above 1 K the Coulomb gap is filled by thermal excitations. This behavior is reflected in the temperature dependence of the variable-range hopping resitivity measured on the same samples: Up to a few degrees Kelvin the Efros-Shkovskii ln$R \propto T^{-1/2}$ law is obeyed, whereas at higher temperatures deviations from this law are observed, indicating a cross-over to Mott's ln$R \propto T^{-1/4}$ law. The mechanism of this cross-over is different from that considered previously in the literature.Comment: 3 pages, 3 figure

A Numerical Study of Transport and Shot Noise at 2D Hopping

We have used modern supercomputer facilities to carry out extensive Monte Carlo simulations of 2D hopping (at negligible Coulomb interaction) in conductors with the completely random distribution of localized sites in both space and energy, within a broad range of the applied electric field $E$ and temperature $T$, both within and beyond the variable-range hopping region. The calculated properties include not only dc current and statistics of localized site occupation and hop lengths, but also the current fluctuation spectrum. Within the calculation accuracy, the model does not exhibit $1/f$ noise, so that the low-frequency noise at low temperatures may be characterized by the Fano factor $F$. For sufficiently large samples, $F$ scales with conductor length $L$ as $(L_c/L)^{\alpha}$, where $\alpha=0.76\pm 0.08 < 1$, and parameter $L_c$ is interpreted as the average percolation cluster length. At relatively low $E$, the electric field dependence of parameter $L_c$ is compatible with the law $L_c\propto E^{-0.911}$ which follows from directed percolation theory arguments.Comment: 17 pages, 8 figures; Fixed minor typos and updated reference