The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform
Paul Emsley - One of the best experts on this subject based on the ideXlab platform.
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current developments in Coot for macromolecular model building of electron cryo microscopy and crystallographic data
Protein Science, 2020Co-Authors: Ana Casanal, Bernhard Lohkamp, Paul EmsleyAbstract:Coot is a tool widely used for model building, refinement, and validation of macromolecular structures. It has been extensively used for crystallography and, more recently, improvements have been introduced to aid in cryo-EM model building and refinement, as cryo-EM structures with resolution ranging 2.5-4 A are now routinely available. Model building into these maps can be time-consuming and requires experience in both biochemistry and building into low-resolution maps. To simplify and expedite the model building task, and minimize the needed expertise, new tools are being added in Coot. Some examples include morphing, Geman-McClure restraints, full-chain refinement, and Fourier-model based residue-type-specific Ramachandran restraints. Here, we present the current state-of-the-art in Coot usage.
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structural analysis of glycoproteins building n linked glycans with Coot
Acta Crystallographica Section D-biological Crystallography, 2018Co-Authors: Paul Emsley, Max CrispinAbstract:Coot is a graphics application that is used to build or manipulate macromolecular models; its particular forte is manipulation of the model at the residue level. The model-building tools of Coot have been combined and extended to assist or automate the building of N-linked glycans. The model is built by the addition of monosaccharides, placed by variation of internal coordinates. The subsequent model is refined by real-space refinement, which is stabilized with modified and additional restraints. It is hoped that these enhanced building tools will help to reduce building errors of N-linked glycans and improve our knowledge of the structures of glycoproteins.
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tools for ligand validation in Coot
Acta Crystallographica Section D Structural Biology, 2017Co-Authors: Paul EmsleyAbstract:Coot is a molecular-graphics program primarily aimed at model building using X-ray data. Recently, tools for the manipulation and representation of ligands have been introduced. Here, these new tools for ligand validation and comparison are described. Ligands in the wwPDB have been scored by density-fit, distortion and atom-clash metrics. The distributions of these scores can be used to assess the relative merits of the particular ligand in the protein–ligand complex of interest by means of `sliders' akin to those now available for each accession code on the wwPDB websites.
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tools for macromolecular model building and refinement into electron cryo microscopy reconstructions
Acta Crystallographica Section D-biological Crystallography, 2015Co-Authors: Alan Brown, Paul Emsley, Fei Long, Robert A Nicholls, Jaan Toots, Garib N MurshudovAbstract:The recent rapid development of single-particle electron cryo-microscopy (cryo-EM) now allows structures to be solved by this method at resolutions close to 3 A. Here, a number of tools to facilitate the interpretation of EM reconstructions with stereochemically reasonable all-atom models are described. The BALBES database has been repurposed as a tool for identifying protein folds from density maps. Modifications to Coot, including new Jiggle Fit and morphing tools and improved handling of nucleic acids, enhance its functionality for interpreting EM maps. REFMAC has been modified for optimal fitting of atomic models into EM maps. As external structural information can enhance the reliability of the derived atomic models, stabilize refinement and reduce overfitting, ProSMART has been extended to generate interatomic distance restraints from nucleic acid reference structures, and a new tool, LIBG, has been developed to generate nucleic acid base-pair and parallel-plane restraints. Furthermore, restraint generation has been integrated with visualization and editing in Coot, and these restraints have been applied to both real-space refinement in Coot and reciprocal-space refinement in REFMAC.
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handling ligands with Coot
Acta Crystallographica Section D-biological Crystallography, 2012Co-Authors: Judit E Debreczeni, Paul EmsleyAbstract:Coot is a molecular-graphics application primarily aimed to assist in model building and validation of biological macromolecules. Recently, tools have been added to work with small molecules. The newly incorporated tools for the manipulation and validation of ligands include interaction with PRODRG, subgraph isomorphism-based tools, representation of ligand chemistry, ligand fitting and analysis, and are described here.
Adam Driks - One of the best experts on this subject based on the ideXlab platform.
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a distance weighted interaction map reveals a previously uncharacterized layer of the bacillus subtilis spore coat
Current Biology, 2010Co-Authors: Peter T Mckenney, Adam Driks, Haig A Eskandarian, Paul Grabowski, Jonathan M Guberman, Katherine H Wang, Zemer Gitai, Patrick EichenbergerAbstract:Bacillus subtilis spores are encased in a protein assembly called the spore coat that is made up of at least 70 different proteins. Conventional electron microscopy shows the coat to be organized into two distinct layers. Because the coat is about as wide as the theoretical limit of light microscopy, quantitatively measuring the localization of individual coat proteins within the coat is challenging. We used fusions of coat proteins to green fluorescent protein to map genetic dependencies for coat assembly and to define three independent subnetworks of coat proteins. To complement the genetic data, we measured coat protein localization at subpixel resolution and integrated these two data sets to produce a distance-weighted genetic interaction map. Using these data, we predict that the coat comprises at least four spatially distinct layers, including a previously uncharacterized glycoprotein outermost layer that we name the spore crust. We found that crust assembly depends on proteins we predicted to localize to the crust. The crust may be conserved in all Bacillus spores and may play critical functions in the environment.
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Bacillus subtilis Spore Coat
Microbiology and Molecular Biology Reviews, 1999Co-Authors: Adam DriksAbstract:In response to starvation, bacilli and clostridia undergo a specialized program of development that results in the production of a highly resistant dormant cell type known as the spore. A proteinacious shell, called the coat, encases the spore and plays a major role in spore survival. The coat is composed of over 25 polypeptide species, organized into several morphologically distinct layers. The mechanisms that guide coat assembly have been largely unknown until recently. We now know that proper formation of the coat relies on the genetic program that guides the synthesis of spore components during development as well as on morphogenetic proteins dedicated to coat assembly. Over 20 structural and morphogenetic genes have been cloned. In this review, we consider the contributions of the known coat and morphogenetic proteins to coat function and assembly. We present a model that describes how morphogenetic proteins direct coat assembly to the specific subcellular site of the nascent spore surface and how they establish the coat layers. We also discuss the importance of posttranslational processing of coat proteins in coat morphogenesis. Finally, we review some of the major outstanding questions in the field.
Jared G Underwood - One of the best experts on this subject based on the ideXlab platform.
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interisland genetic structure of two endangered hawaiian waterbirds the hawaiian Coot and hawaiian gallinule
The Condor, 2018Co-Authors: Sarah A Sonsthagen, Robert E Wilson, Jared G UnderwoodAbstract:ABSTRACT Most of Hawaii's endemic avifauna are species of conservation concern. Some of Hawaii's endangered waterbirds, however, have increased in number as a result of intensive management of wetlands. To inform these conservation efforts, we examined interisland genetic structure and gene flow within 2 Hawaiian endemic waterbirds, the Hawaiian Coot (Fulica alai) and the Hawaiian subspecies of the Common Gallinule (Gallinula galeata sandvicensis), using microsatellite and mitochondrial loci. Hawaiian Coots and Hawaiian Gallinules occupy coastal wetlands and exhibit similar life history characteristics and generation times, although they may differ in dispersal propensity. Mark–resight data for Hawaiian Coot indicate interisland movements, whereas Hawaiian Gallinules are sedentary. Genetic diversity is partitioned across the landscape differently for Hawaiian Coots and Hawaiian Gallinules; patterns of variation are likely influenced by behavioral and ecological mechanisms. Hawaiian Coots exhibit low level...
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genetic implications of bottleneck effects of differing severities on genetic diversity in naturally recovering populations an example from hawaiian Coot and hawaiian gallinule
Ecology and Evolution, 2017Co-Authors: Sarah A Sonsthagen, Robert E Wilson, Jared G UnderwoodAbstract:The evolutionary trajectory of populations through time is influenced by the interplay of forces (biological, evolutionary, and anthropogenic) acting on the standing genetic variation. We used microsatellite and mitochondrial loci to examine the influence of population declines, of varying severity, on genetic diversity within two Hawaiian endemic waterbirds, the Hawaiian Coot and Hawaiian gallinule, by comparing historical (samples collected in the late 1800s and early 1900s) and modern (collected in 2012-2013) populations. Population declines simultaneously experienced by Hawaiian Coots and Hawaiian gallinules differentially shaped the evolutionary trajectory of these two populations. Within Hawaiian Coot, large reductions (between -38.4% and -51.4%) in mitochondrial diversity were observed, although minimal differences were observed in the distribution of allelic and haplotypic frequencies between sampled time periods. Conversely, for Hawaiian gallinule, allelic frequencies were strongly differentiated between time periods, signatures of a genetic bottleneck were detected, and biases in means of the effective population size were observed at microsatellite loci. The strength of the decline appears to have had a greater influence on genetic diversity within Hawaiian gallinule than Hawaiian Coot, coincident with the reduction in census size. These species exhibit similar life history characteristics and generation times; therefore, we hypothesize that differences in behavior and colonization history are likely playing a large role in how allelic and haplotypic frequencies are being shaped through time. Furthermore, differences in patterns of genetic diversity within Hawaiian Coot and Hawaiian gallinule highlight the influence of demographic and evolutionary processes in shaping how species respond genetically to ecological stressors.
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development and characterization of microsatellite markers for the hawaiian Coot fulica alai and hawaiian gallinule gallinula galeata sandvicensis through next generation sequencing
Conservation Genetics Resources, 2014Co-Authors: Sarah A Sonsthagen, Robert E Wilson, Jared G UnderwoodAbstract:We used next generation shotgun sequencing to develop novel microsatellite markers for two endangered waterbirds; the Hawaiian Coot (Fulica alai) and Hawaiian gallinule (Gallinula galeata sandvicensis). The 20 loci polymorphic in the Hawaiian Coot displayed moderate allelic diversity (average 3.8 alleles/locus) and heterozygosity (average 59.5 %). The 12 loci variable for the Hawaiian gallinule exhibited lower levels of allelic diversity (average 2.4 alleles/locus) and heterozygosity (average 47.5 %). Loci were in linkage equilibrium and only one locus deviated from Hardy–Weinberg equilibrium. These loci are sufficiently variable to assess levels of genetic diversity and will be useful for conservation genetic studies to aid in the management of these endangered waterbirds.
Kevin Cowtan - One of the best experts on this subject based on the ideXlab platform.
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features and development of Coot
Acta Crystallographica Section D-biological Crystallography, 2010Co-Authors: Paul Emsley, Bernhard Lohkamp, William G Scott, Kevin CowtanAbstract:Coot is a molecular-graphics application for model building and validation of biological macromolecules. The program displays electron-density maps and atomic models and allows model manipulations such as idealization, real-space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers and Ramachandran idealization. Furthermore, tools are provided for model validation as well as interfaces to external programs for refinement, validation and graphics. The software is designed to be easy to learn for novice users, which is achieved by ensuring that tools for common tasks are `discoverable' through familiar user-interface elements (menus and toolbars) or by intuitive behaviour (mouse controls). Recent developments have focused on providing tools for expert users, with customisable key bindings, extensions and an extensive scripting interface. The software is under rapid development, but has already achieved very widespread use within the crystallographic community. The current state of the software is presented, with a description of the facilities available and of some of the underlying methods employed.
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macromolecular model building and validation using Coot
Acta Crystallographica Section A, 2008Co-Authors: Paul Emsley, Bernhard Lohkamp, Kevin CowtanAbstract:The Coot software package is a tool for interactive macromolecular model building and validation. The software is designed to be easy to learn for novice users by ensuring that tools for common tasks are ‘discoverable’ without consulting the documentation, while also providing enhanced usability for experts through customizable key bindings and extensive scripting interfaces. These considerations have resulted in substantial use throughout the crystallographic community. Coot displays electron-density maps and atomic models, and allows model manipulations such as idealization, real-space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers and Ramachandran idealization. Several of the most important tools are described together with the underlying methods employed. Keywords: Coot; model building; validation
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Coot: Model-building tools for molecular graphics
Acta Crystallographica Section D: Biological Crystallography, 2004Co-Authors: Paul Emsley, Kevin CowtanAbstract:CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality graphics. The map-fitting tools are available as a stand-alone package, distributed as 'Coot'.
Christine Cavazza - One of the best experts on this subject based on the ideXlab platform.
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Biophysical and structural characterization of the putative nickel chaperone Coot from Carboxydothermus hydrogenoformans.
Journal of Biological Inorganic Chemistry, 2018Co-Authors: Marila Alfano, Julien Pérard, Roger Miras, Patrice Catty, Christine CavazzaAbstract:Carboxydothermus hydrogenoformans is a model microorganism for the study of [NiFe]-CODH, a key enzyme of carbon cycle in anaerobic microorganisms. The enzyme possesses a unique active site (C-cluster), constituted of a distorted [NiFe3S4] cubane linked to a mononuclear Fe(II) center. Both the biogenesis of the C-cluster and the activation of CODH by nickel insertion remain unclear. Among the three accessory proteins thought to play a role in this latter step (CooC, CooJ, and Coot), Coot is identified as a nickel chaperone involved in CODH maturation in Rhodospirillum rubrum. Here, we structurally and biophysically characterized a putative Coot protein present in C. hydrogenoformans (pChCoot). Despite the low sequence homologies between Coot from R. rubrum (RrCoot) and pChCoot (19% sequence identity), the two proteins share several similarities, such as their overall structure and a solvent-exposed Ni(II)-binding site at the dimer interface. Moreover, the X-ray structure of pChCoot reveals the proximity between the histidine 55, a potential nickel-coordinating residue, and the cysteine 2, a highly conserved key residue in Ni(II)-binding.
