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1.
Acta Crystallogr D Biol Crystallogr ; 66(Pt 4): 486-501, 2010 Apr.
Article in English | MEDLINE | ID: mdl-20383002

ABSTRACT

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.


Subject(s)
Crystallography, X-Ray/methods , Software Design , DNA/analysis , DNA/chemistry , Models, Molecular , Nucleic Acid Conformation , Protein Structure, Tertiary , Proteins/analysis , Proteins/chemistry , RNA/analysis , RNA/chemistry
2.
Nucleosides Nucleotides Nucleic Acids ; 27(6): 809-15, 2008 Jun.
Article in English | MEDLINE | ID: mdl-18600544

ABSTRACT

A patient with hematuria was shown to have thymine-uraciluria. The dihydropyrimidine dehydrogenase (DPD) activity in peripheral blood mononuclear cells was 0.16 nmol/mg/h; controls: 9.9 +/- 2.8 nmol/mg/h. Analysis of DPYD showed that the patient was compound heterozygous for the novel mutations 237C > A (C79X) in exon 4 and 704G > A (R235Q) in exon 7. The nonsense mutation (C79X) leads to premature termination of translation and thus to a non-functional protein. Analysis of the crystal structure of pig DPD suggested that the R235Q mutation might interfere with the binding of FAD and the electron flow between the NADPH and the pyrimidine substrate site of DPD.


Subject(s)
Dihydrouracil Dehydrogenase (NADP)/genetics , Hematuria/enzymology , Hematuria/genetics , Mutation, Missense , Point Mutation , Adult , Animals , Child , Crystallography, X-Ray , Dihydrouracil Dehydrogenase (NADP)/chemistry , Dihydrouracil Dehydrogenase (NADP)/metabolism , Female , Genotype , Hematuria/pathology , Humans , Male , Models, Molecular , Protein Conformation , Swine
3.
J Biol Chem ; 276(23): 19954-8, 2001 Jun 08.
Article in English | MEDLINE | ID: mdl-11278676

ABSTRACT

Hemocyanins are multisubunit respiratory proteins found in many invertebrates. They bind oxygen highly cooperatively. However, not much is known about the structural basis of this behavior. We studied the influence of the physiological allosteric effector l-lactate on the oxygenated quaternary structure of the 2x6-meric hemocyanin from the lobster Homarus americanus employing small angle x-ray scattering (SAXS). The presence of 20 mm l-lactate resulted in different scattering curves compared with those obtained in the absence of l-lactate. The distance distribution functions p(r) indicated a more compact molecule in presence of l-lactate, which is also reflected in a reduction of the radius of gyration by about 0.2 nm (3%). Thus, we show for the first time on a structural basis that a hemocyanin in the oxy state can adopt two different conformations. This is as predicted from the analysis of oxygen binding curves according to the "nesting" model. A comparison of the distance distribution functions p(r) obtained from SAXS with those deduced from electron microscopy revealed large differences. The distance between the two hexamers as deduced from electron microscopy has to be shortened by up to 1.1 nm to agree well with the small angle x-ray curves.


Subject(s)
Hemocyanins/chemistry , Lactic Acid/metabolism , Allosteric Regulation , Animals , Hemocyanins/metabolism , Hemocyanins/ultrastructure , Microscopy, Electron , Nephropidae , Protein Conformation , Scattering, Radiation
4.
Acta Crystallogr D Biol Crystallogr ; 56(Pt 11): 1488-91, 2000 Nov.
Article in English | MEDLINE | ID: mdl-11185885

ABSTRACT

ATP-phosphoribosyltransferase (ATP-PRT) from Escherichia coli has been purified and crystals were obtained by the vapour-diffusion method using sodium tartrate as a precipitant. Dynamic light scattering was used to assess conditions for the monodispersity of the enzyme. The crystals are trigonal, space group R32, with unit-cell parameters a = b = 133.6, c= 114.1 A (at 100 K), and diffract to 2.7 A on a synchrotron X-ray source. The asymmetric unit is likely to contain one molecule, corresponding to a packing density of 2.9 A3 Da(-1). A model for the quaternary structure is proposed based on the crystallographic symmetry.


Subject(s)
ATP Phosphoribosyltransferase/isolation & purification , Escherichia coli/enzymology , ATP Phosphoribosyltransferase/chemistry , Crystallization , Crystallography, X-Ray , Light , Models, Molecular , Protein Conformation , Scattering, Radiation
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