X-Ray Diffraction and Molecular Model Building Studies of The Interaction of Actinomycin with Nucleic Acids

Nature ◽  
1963 ◽  
Vol 198 (4880) ◽  
pp. 538-540 ◽  
Author(s):  
L. D. HAMILTON ◽  
W. FULLER ◽  
E. REICH
Keyword(s):  
Nucleic Acids ◽  
Model Building ◽  
Molecular Model ◽  
X Ray Diffraction ◽  
X Ray

scholarly journals The dimensions and shapes of the furanose rings in nucleic acids

1972 ◽  
Vol 130 (2) ◽  
pp. 453-465 ◽  
Author(s):  
S. Arnott ◽  
D. W. L. Hukins
Keyword(s):  
Nucleic Acids ◽  
Model Building ◽  
Molecular Model ◽  
Relative Orientation ◽  
Ring Conformation ◽  
Mean Values ◽  
Pyrimidine Base ◽  
X Ray ◽  
X Ray Crystallography ◽  
Ring Puckering

A survey was made of the geometry of furanose rings in β-nucleotides and β-nucleosides (as monomers related to nucleic acids) for which structures have been determined by X-ray crystallography. Mean values, and estimated standard deviations from them, were calculated for bond-lengths, bond-angles and conformation-angles. For parameters with values dependent on ring-puckering, separate calculations were made for each ring type. (The rings are puckered in one of three conformations: C-2- or C-3-endo or C-3-exo; C-2-exo has not been observed.) The results were used to compute standard furanose rings with C-2-endo, C-3-endo and C-3-exo conformations for use in nucleic acid molecular model-building. The survey also showed that the only other conformation-angle in nucleotides dependent on the furanose ring conformation corresponds to the relative orientation of the purine (or pyrimidine) base and the ring.

scholarly journals Vagabond: bond-based parametrization reduces overfitting for refinement of proteins

2021 ◽  
Vol 77 (4) ◽  
Author(s):  
Helen M. Ginn
Keyword(s):  
Model Building ◽  
Molecular Model ◽  
Biological Information ◽  
Complex Structures ◽  
X Ray Diffraction ◽  
Worst Case ◽  
X Ray ◽  
Density Maps ◽  
Current Implementation ◽  
Almost All

Structural biology methods have delivered over 150 000 high-resolution structures of macromolecules, which have fundamentally altered our understanding of biology and our approach to developing new medicines. However, the description of molecular flexibility is instrinsically flawed and in almost all cases, regardless of the experimental method used for structure determination, there remains a strong overfitting bias during molecular model building and refinement. In the worst case this can lead to wholly incorrect structures and thus incorrect biological interpretations. Here, by reparametrizing the description of these complex structures in terms of bonds rather than atomic positions, and by modelling flexibility using a deterministic ensemble of structures, it is demonstrated that structures can be described using fewer parameters than in conventional refinement. The current implementation, applied to X-ray diffraction data, significantly reduces the extent of overfitting, allowing the experimental data to reveal more biological information in electron-density maps.

Comparative X-Ray Studies on the Interaction of Carotenoids with a Model Phosphatidylcholine Membrane

2002 ◽  
Vol 57 (1-2) ◽  
pp. 129-134 ◽  
Author(s):  
Mario Faculty of Chemical Sciences, Unive ◽  
Paulina Hidalgo ◽  
Kazimierz Strzalka ◽  
Anna Kostecka-Gugala
Keyword(s):  
Structural Damage ◽  
Molecular Model ◽  
Acyl Chain ◽  
Aqueous Media ◽  
Molecular Characteristics ◽  
Hydrophobic Core ◽  
X Ray Diffraction ◽  
X Ray ◽  
Epoxy Groups ◽  
Β Carotene

The interaction of structurally different carotenoids with a membrane molecular model was examined by X-ray diffraction. The selected compounds were β-carotene, lycopene, lutein, violaxanthin, zeaxanthin, and additionally carotane, a fully saturated derivative of β-carotene. They present similarities and differences in their rigidity, the presence of terminal ionone rings and hydroxy and epoxy groups bound to the rings. The membrane models were multibilayers of dipalmitoylphosphatidylcholine (DPPC), chosen for this investigation because the 3 nm thickness of the hydrophobic core of its bilayer coincides with the thickness of the hydrophobic core of thylakoid membranes and the length of the carotenoid molecules. Results indicate that the six compounds induced different types and degrees of structural perturbations to DPPC bilayers in aqueous media. They were interpreted in terms of the molecular characteristics of DPPC and the carotenoids. Lycopene and violaxanthin induced the highest structural damage to the acyl chain and polar headgroup regions of DPPC bilayers, respectively.

scholarly journals Macromolecular crystallography using neutrons

2014 ◽  
Vol 36 (3) ◽  
pp. 40-42
Author(s):  
Matthew Blakeley
Keyword(s):  
Nucleic Acids ◽  
Biological Systems ◽  
Biological Macromolecules ◽  
X Rays ◽  
Macromolecular Crystallography ◽  
X Ray Diffraction ◽  
Vast Array ◽  
X Ray ◽  
Macromolecular Assemblies

When you think about macromolecular crystallography, the technique that most often comes to mind is X-ray diffraction and it's no wonder. Over 88000 structures of biological macromolecules – from proteins and nucleic acids to viruses and macromolecular assemblies – have been determined using X-rays, and these have contributed significantly to our understanding of a vast array of biological systems and processes.

scholarly journals Solving a new R2lox protein structure by microcrystal electron diffraction

2019 ◽  
Vol 5 (8) ◽  
pp. eaax4621 ◽  
Author(s):  
Hongyi Xu ◽  
Hugo Lebrette ◽  
Max T. B. Clabbers ◽  
Jingjing Zhao ◽  
Julia J. Griese ◽  
...  
Keyword(s):  
Protein Structure ◽  
Electron Diffraction ◽  
Model Building ◽  
Protein Structures ◽  
X Ray Diffraction ◽  
X Ray ◽  
X Ray Crystallography ◽  
Potential Map ◽  
Metal Cofactor ◽  
And Function

Microcrystal electron diffraction (MicroED) has recently shown potential for structural biology. It enables the study of biomolecules from micrometer-sized 3D crystals that are too small to be studied by conventional x-ray crystallography. However, to date, MicroED has only been applied to redetermine protein structures that had already been solved previously by x-ray diffraction. Here, we present the first new protein structure—an R2lox enzyme—solved using MicroED. The structure was phased by molecular replacement using a search model of 35% sequence identity. The resulting electrostatic scattering potential map at 3.0-Å resolution was of sufficient quality to allow accurate model building and refinement. The dinuclear metal cofactor could be located in the map and was modeled as a heterodinuclear Mn/Fe center based on previous studies. Our results demonstrate that MicroED has the potential to become a widely applicable tool for revealing novel insights into protein structure and function.

The helical structure of the β -1, 3-linked xylan in some siphoneous green algae

1969 ◽  
Vol 173 (1031) ◽  
pp. 209-221 ◽  
Keyword(s):  
Green Algae ◽  
Cell Walls ◽  
Model Building ◽  
Hexagonal Lattice ◽  
Bound Water ◽  
Helical Structure ◽  
Polymer Chains ◽  
X Ray Diffraction ◽  
X Ray ◽  
Fixed Orientation

An account is given of the conformation of a β -1, 3-linked xylan which is the structural poly-saccharide in some siphoneous green algae. The cell walls from Penicillus dumetosus were studied by X -ray diffraction, infra-red absorption and model building. The structure consists of three xylan polymer chains intertwining to form a three-strand helix with symmetry sr. Each helix has six xylose residues per turn in a pitch of approximately 18 Å. A novel type of inter-chain bonding has been proposed which consists of a cyclic triad of hydrogen bonds formed between the O 2 atoms, one from each individual chain. Computations show that the molecules are in fixed orientation in a hexagonal lattice. The calculations favour right-handed helices and there is evidence of stoichiometrically bound water on the surface of the molecule.

Polymorphism of naphthazarin and its relation to solid-state proton transfer. Neutron and X-ray diffraction studies on naphthazarin C

1985 ◽  
Vol 399 (1817) ◽  
pp. 295-319 ◽  
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Solid State ◽  
Neutron Diffraction ◽  
Room Temperature ◽  
Model Comparison ◽  
Molecular Model ◽  
Molecular Formula ◽  
X Ray Diffraction ◽  
X Ray

The crystal structure of naphthazarin C has been determined by neutron diffraction at 60 and 300 K (λ ═ 0.895 Å; 1 Å ═ 10 -10 m ═ 10 -1 nm) and X-ray diffraction at 300 K. The space group is Pc at 60 K, but P 2 1 /c at 300 K. There are small but significant differences in cell dimensions at the two temperatures: a ═ 7.664 (7.915), b ═ 7.304 (7.262), c ═ 15.16 (15.284) Å; β ═ 114.60 (114.20)°; Z ═ 4; U ═ 771.6 (801.3) Å 3 (values at 300 K in parentheses). Neutron diffraction shows that the Pc and P 2 1 /c structures are related by an order-disorder transition at 110±1 K. Structure analysis (1771 reflections; R F ═ 0.035; R W ═ 0.036) showed that the hydroxyl hydrogens are largely ordered at 60 K, the appropriate molecular formula being 5, 8-dihydroxy-1, 4-naphthadione. Neutron diffraction measurements at 300 K (1769 reflections; R F ═ 0.052) indicated a disordered molecular model with one-half of an hydrogen atom attached to each oxygen. X -ray diffraction measurements on naphthazarin C at 300 K (two independent sets of intensity measurements, one with CuKα and the other with MoKα) support this disordered model. The molecular dimensions for naphthazarin A and B also fit this model. Comparison of the crystal structure of naphthazarin C with those of the A and B polymorphs shows that only the former has intermolecular O─H • • • O hydrogen bonding. The diffraction results combined with the available solid-state n. m. r. data show that there is at room temperature a rapid intramolecular exchange of hydroxylic protons between each pair of oxygen atoms in all three naphthazarin polymorphs. Many 1, 3-diketones exist in an enol form in the solid. These enol forms have been reported to be disordered for about twenty molecules at room temperature (this total includes one molecule studied at 108 K, and four amino-imino systems) and ordered systems have been reported for about fifteen molecules. Intermolecular hydrogen bonding occurs only in a few of these crystals.

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