scholarly journals Combinatorial use of disulfide bridges and native sulfur-SAD phasing for rapid structure determination of coiled-coils

2018 ◽  
Vol 38 (5) ◽  
Author(s):  
Sebastian H.W. Kraatz ◽  
Sarah Bianchi ◽  
Michel O. Steinmetz
Keyword(s):  
Coiled Coil ◽  
Coiled Coils ◽  
Molecular Replacement ◽  
Disulfide Bridges ◽  
X Ray ◽  
X Ray Crystallography ◽  
Protein Protein Interaction ◽  
Eukaryotic Proteins ◽  
Sad Phasing

Coiled-coils are ubiquitous protein–protein interaction motifs found in many eukaryotic proteins. The elongated, flexible and often irregular nature of coiled-coils together with their tendency to form fibrous arrangements in crystals imposes challenges on solving the phase problem by molecular replacement. Here, we report the successful combinatorial use of native and rational engineered disulfide bridges together with sulfur-SAD phasing as a powerful tool to stabilize and solve the structure of coiled-coil domains in a straightforward manner. Our study is a key example of how modern sulfur SAD combined with mutagenesis can help to advance and simplify the structural study of challenging coiled-coil domains by X-ray crystallography.

scholarly journals From lows to highs: using low-resolution models to phase X-ray data

2013 ◽  
Vol 69 (11) ◽  
pp. 2257-2265 ◽  
Author(s):  
David I. Stuart ◽  
Nicola G. A. Abrescia
Keyword(s):  
Structural Biology ◽  
General Concept ◽  
Molecular Replacement ◽  
X Ray ◽  
X Ray Crystallography ◽  
X Ray Scattering ◽  
Phase Extension ◽  
Intact Virus ◽  
Structural Methods

The study of virus structures has contributed to methodological advances in structural biology that are generally applicable (molecular replacement and noncrystallographic symmetry are just two of the best known examples). Moreover, structural virology has been instrumental in forging the more general concept of exploiting phase information derived from multiple structural techniques. This hybridization of structural methods, primarily electron microscopy (EM) and X-ray crystallography, but also small-angle X-ray scattering (SAXS) and nuclear magnetic resonance (NMR) spectroscopy, is central to integrative structural biology. Here, the interplay of X-ray crystallography and EM is illustrated through the example of the structural determination of the marine lipid-containing bacteriophage PM2. Molecular replacement starting from an ∼13 Å cryo-EM reconstruction, followed by cycling density averaging, phase extension and solvent flattening, gave the X-ray structure of the intact virus at 7 Å resolution This in turn served as a bridge to phase, to 2.5 Å resolution, data from twinned crystals of the major coat protein (P2), ultimately yielding a quasi-atomic model of the particle, which provided significant insights into virus evolution and viral membrane biogenesis.

Structure determination of the nucleosome core particle by selenium SAD phasing

2019 ◽  
Vol 75 (10) ◽  
pp. 930-936
Author(s):  
Mika Saotome ◽  
Naoki Horikoshi ◽  
Kazuki Urano ◽  
Tomoya Kujirai ◽  
Hidetaka Yuzurihara ◽  
...  
Keyword(s):  
Molecular Replacement ◽  
Base Pairs ◽  
Simple Method ◽  
X Ray Crystallography ◽  
Nucleosome Core ◽  
Nucleosome Core Particles ◽  
Experimental Phasing ◽  
Eukaryotic Species ◽  
Sad Phasing

The eukaryotic genome is compacted inside the nucleus of the cell in the form called chromatin. The fundamental unit of chromatin is the nucleosome, which contains four types of histones (H3, H4, H2A and H2B) and approximately 150 base pairs of DNA wrapped around the histone complex. The structure of the nucleosome is highly conserved across several eukaryotic species, and molecular replacement has been the primary phasing method used to solve nucleosome structures by X-ray crystallography. However, there is currently no simple, widely applicable experimental phasing method for the nucleosome. In the present study, it is demonstrated that selenomethionine-incorporated histones H3, H2A and H2B can be reconstituted into nucleosomes and crystallized for structural determination. Unexpectedly, it was found that the nucleosome can be phased with a relatively small number of Se atoms. The structures of nucleosome core particles containing 12 and 16 Se atoms were solved by SAD phasing at 2.5 and 2.4 Å resolution, respectively. The present study demonstrates a simple method for determining nucleosome structures by experimental phasing, which may be particularly useful for noncanonical structures that cannot be solved by molecular replacement.

scholarly journals Extending the scope of coiled-coil crystal structure solution by AMPLE through improved ab initio modelling

2020 ◽  
Vol 76 (3) ◽  
pp. 272-284 ◽  
Author(s):  
Jens M. H. Thomas ◽  
Ronan M. Keegan ◽  
Daniel J. Rigden ◽  
Owen R. Davies
Keyword(s):  
Ab Initio ◽  
Coiled Coil ◽  
Coiled Coils ◽  
Molecular Replacement ◽  
Helical Structures ◽  
Major Barrier ◽  
X Ray Crystallography ◽  
Structure Solution ◽  
Coil Structure ◽  
Experimental Phasing

The phase problem remains a major barrier to overcome in protein structure solution by X-ray crystallography. In recent years, new molecular-replacement approaches using ab initio models and ideal secondary-structure components have greatly contributed to the solution of novel structures in the absence of clear homologues in the PDB or experimental phasing information. This has been particularly successful for highly α-helical structures, and especially coiled-coils, in which the relatively rigid α-helices provide very useful molecular-replacement fragments. This has been seen within the program AMPLE, which uses clustered and truncated ensembles of numerous ab initio models in structure solution, and is already accomplished for α-helical and coiled-coil structures. Here, an expansion in the scope of coiled-coil structure solution by AMPLE is reported, which has been achieved through general improvements in the pipeline, the removal of tNCS correction in molecular replacement and two improved methods for ab initio modelling. Of the latter improvements, enforcing the modelling of elongated helices overcame the bias towards globular folds and provided a rapid method (equivalent to the time requirements of the existing modelling procedures in AMPLE) for enhanced solution. Further, the modelling of two-, three- and four-helical oligomeric coiled-coils, and the use of full/partial oligomers in molecular replacement, provided additional success in difficult and lower resolution cases. Together, these approaches have enabled the solution of a number of parallel/antiparallel dimeric, trimeric and tetrameric coiled-coils at resolutions as low as 3.3 Å, and have thus overcome previous limitations in AMPLE and provided a new functionality in coiled-coil structure solution at lower resolutions. These new approaches have been incorporated into a new release of AMPLE in which automated elongated monomer and oligomer modelling may be activated by selecting `coiled-coil' mode.

Electron microscopy of rabbit FC crystals

1983 ◽  
Vol 41 ◽  
pp. 730-731
Author(s):  
Robert A. Grant ◽  
Laura L. Degn ◽  
Wah Chiu ◽  
John Robinson
Keyword(s):  
Electron Microscopy ◽  
High Resolution ◽  
High Resolution Electron Microscopy ◽  
Molecular Replacement ◽  
X Ray ◽  
X Ray Crystallography ◽  
Resolution Electron ◽  
Replacement Technique ◽  
Hydrated Crystal ◽  
Molecular Structure Analysis

Proteolytic digestion of the immunoglobulin IgG with papain cleaves the molecule into an antigen binding fragment, Fab, and a compliment binding fragment, Fc. Structures of intact immunoglobulin, Fab and Fc from various sources have been solved by X-ray crystallography. Rabbit Fc can be crystallized as thin platelets suitable for high resolution electron microscopy. The structure of rabbit Fc can be expected to be similar to the known structure of human Fc, making it an ideal specimen for comparing the X-ray and electron crystallographic techniques and for the application of the molecular replacement technique to electron crystallography. Thin protein crystals embedded in ice diffract to high resolution. A low resolution image of a frozen, hydrated crystal can be expected to have a better contrast than a glucose embedded crystal due to the larger density difference between protein and ice compared to protein and glucose. For these reasons we are using an ice embedding technique to prepare the rabbit Fc crystals for molecular structure analysis by electron microscopy.

Synthesis of enantiopure 2-aryl-2-methoxypropionic acids and determination of their absolute configurations by X-ray crystallography

Chirality ◽  
2008 ◽  
Vol 20 (3-4) ◽  
pp. 251-264 ◽  
Author(s):  
Satoshi Sekiguchi ◽  
Junpei Naito ◽  
Hiromi Taji ◽  
Yusuke Kasai ◽  
Akinori Sugio ◽  
...  
Keyword(s):  
X Ray ◽  
X Ray Crystallography

scholarly journals Unraveling the long-pursued Au144 structure by x-ray crystallography

2018 ◽  
Vol 4 (10) ◽  
pp. eaat7259 ◽  
Author(s):  
Nan Yan ◽  
Nan Xia ◽  
Lingwen Liao ◽  
Min Zhu ◽  
Fengming Jin ◽  
...  
Keyword(s):  
Metal Nanoparticles ◽  
Weak Interactions ◽  
Gold Nanoclusters ◽  
Atomic Level ◽  
High Quality ◽  
X Ray ◽  
X Ray Crystallography ◽  
Quantum Size ◽  
First Time

The transition from nanocluster to nanocrystal is a central issue in nanoscience. The atomic structure determination of metal nanoparticles in the transition size range is challenging and particularly important in understanding the quantum size effect at the atomic level. On the basis of the rationale that the intra- and interparticle weak interactions play critical roles in growing high-quality single crystals of metal nanoparticles, we have reproducibly obtained ideal crystals of Au144(SR)60 and successfully solved its structure by x-ray crystallography (XRC); this structure was theoretically predicted a decade ago and has long been pursued experimentally but without success until now. Here, XRC reveals an interesting Au12 hollow icosahedron in thiolated gold nanoclusters for the first time. The Au–Au bond length, close to that of bulk gold, shows better thermal extensibility than the other Au–Au bond lengths in Au144(SR)60, providing an atomic-level perspective because metal generally shows better thermal extensibility than nonmetal materials. Thus, our work not only reveals the mysterious, long experimentally pursued structure of a transition-sized nanoparticle but also has important implications for the growth of high-quality, single-crystal nanoparticles, as well as for the understanding of the thermal extensibility of metals from the perspective of chemical bonding.

ChemInform Abstract: Synthesis of cis-1-((2-Hydroxymethyl)cyclopentyl)uracil and Determination of Its Conformation by X-Ray Crystallography and AM1 Theoretical Calculations.

ChemInform ◽  
2010 ◽  
Vol 27 (43) ◽  
pp. no-no
Author(s):  
L. SANTANA ◽  
M. TEIJEIRA ◽  
E. URIARTE ◽  
C. TERAN ◽  
U. CASELLATO ◽  
...  
Keyword(s):  
Theoretical Calculations ◽  
X Ray ◽  
X Ray Crystallography

scholarly journals Characterization of reactive organometallic species via MicroED

2019 ◽  
Author(s):  
Christopher Jones ◽  
Matthew Asay ◽  
Lee Joon Kim ◽  
Jack Kleinsasser ◽  
Ambarneil Saha ◽  
...  
Keyword(s):  
Transition Metal ◽  
Metal Complexes ◽  
Transition Metal Complexes ◽  
Cryogenic Cooling ◽  
Structural Determination ◽  
X Ray ◽  
X Ray Crystallography ◽  
Diamagnetic Transition

Here we apply microcrystal electron diffraction (MicroED) to the structural determination of transition metal complexes. We find that the simultaneous use of 300 keV electrons, very low electron doses, and an ultra-sensitive camera allows for the collection of data without cryogenic cooling of the stage. This technique reveals the first crystal structures of the classic zirconocene hydride, colloquially known as “Schwartz’s reagent”, a novel Pd(II) complex not amenable to solution-state NMR or X-ray crystallography, and five other paramagnetic or diamagnetic transition metal complexes.

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