scholarly journals Elucidation of a nutlin-derivative—HDM2 complex structure at the interaction site by NMR Molecular Replacement: a straightforward derivation

2022 ◽  
pp. 100032
Author(s):  
Valerie Mertens ◽  
Marie José Abi Saad ◽  
Nicolas Coudevylle ◽  
Marielle Aulikki Wälti ◽  
Aaron Finke ◽  
...  
Keyword(s):  
Complex Structure ◽  
Molecular Replacement ◽  
Interaction Site

scholarly journals Crystal Structure of the Terminal Oxygenase Component of Cumene Dioxygenase from Pseudomonas fluorescens IP01

2005 ◽  
Vol 187 (7) ◽  
pp. 2483-2490 ◽  
Author(s):  
Xuesong Dong ◽  
Shinya Fushinobu ◽  
Eriko Fukuda ◽  
Tohru Terada ◽  
Shugo Nakamura ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Pseudomonas Fluorescens ◽  
Active Site ◽  
Complex Structure ◽  
Binding Pocket ◽  
Nonheme Iron ◽  
Single Amino Acid ◽  
Molecular Replacement ◽  
Catalytic Subunits ◽  
Single Amino Acid Residue

ABSTRACT The crystal structure of the terminal component of the cumene dioxygenase multicomponent enzyme system of Pseudomonas fluorescens IP01 (CumDO) was determined at a resolution of 2.2 Å by means of molecular replacement by using the crystal structure of the terminal oxygenase component of naphthalene dioxygenase from Pseudomonas sp. strain NCIB 9816-4 (NphDO). The ligation of the two catalytic centers of CumDO (i.e., the nonheme iron and Rieske [2Fe-2S] centers) and the bridging between them in neighboring catalytic subunits by hydrogen bonds through a single amino acid residue, Asp231, are similar to those of NphDO. An unidentified external ligand, possibly dioxygen, was bound at the active site nonheme iron. The entrance to the active site of CumDO is different from the entrance to the active site of NphDO, as the two loops forming the lid exhibit great deviation. On the basis of the complex structure of NphDO, a biphenyl substrate was modeled in the substrate-binding pocket of CumDO. The residues surrounding the modeled biphenyl molecule include residues that have already been shown to be important for its substrate specificity by a number of engineering studies of biphenyl dioxygenases.

scholarly journals Protein-complex structure completion usingIPCAS(Iterative Protein Crystal structure Automatic Solution)

2015 ◽  
Vol 71 (7) ◽  
pp. 1487-1492 ◽  
Author(s):  
Weizhe Zhang ◽  
Hongmin Zhang ◽  
Tao Zhang ◽  
Haifu Fan ◽  
Quan Hao
Keyword(s):  
Crystal Structure ◽  
Protein Complex ◽  
Model Building ◽  
Protein Complexes ◽  
Direct Method ◽  
Complex Structure ◽  
Protein Crystal ◽  
Molecular Replacement ◽  
Protein Crystal Structure ◽  
Building Program

Protein complexes are essential components in many cellular processes. In this study, a procedure to determine the protein-complex structure from a partial molecular-replacement (MR) solution is demonstrated using a direct-method-aided dual-space iterative phasing and model-building program suite,IPCAS(Iterative Protein Crystal structure Automatic Solution). TheIPCASiteration procedure involves (i) real-space model building and refinement, (ii) direct-method-aided reciprocal-space phase refinement and (iii) phase improvement through density modification. The procedure has been tested with four protein complexes, including two previously unknown structures. It was possible to useIPCASto build the whole complex structure from one or less than one subunit once the molecular-replacement method was able to give a partial solution. In the most challenging case,IPCASwas able to extend to the full length starting from less than 30% of the complex structure, while conventional model-building procedures were unsuccessful.

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.

A new method of complex structure analysis by electron microscopy

1978 ◽  
Vol 36 (1) ◽  
pp. 628-629
Author(s):  
V.V. Rybin ◽  
E.V. Voronina
Keyword(s):  
Complex Structure ◽  
Reciprocal Lattice ◽  
Stacking Faults ◽  
Plastic Strains ◽  
Base Position ◽  
Structural Regularity ◽  
Orientation Matrix ◽  
Computerized Processing ◽  
Fully Automatic ◽  
Diffraction Patterns

Recently, it has become essential to develop a helpful method of the complete crystallographic identification of fine fragmented crystals. This was maainly due to the investigation into structural regularity of large plastic strains. The method should be practicable for determining crystallographic orientation (CO) of elastically stressed micro areas of the order of several micron fractions in size and filled with λ>1010 cm-2 density dislocations or stacking faults. The method must provide the misorientation vectors of the adjacent fragments when the angle ω changes from 0 to 180° with the accuracy of 0,3°. The problem is that the actual electron diffraction patterns obtained from fine fragmented crystals are the superpositions of reflections from various fragments, though more than one or two reflections from a fragment are hardly possible. Finally, the method should afford fully automatic computerized processing of the experimental results.The proposed method meets all the above requirements. It implies the construction for a certain base position of the crystal the orientation matrix (0M) A, which gives a single intercorrelation between the coordinates of the unity vector in the reference coordinate system (RCS) and those of the same vector in the crystal reciprocal lattice base : .

Computer processing of high-resolution images of periodic specimens

1986 ◽  
Vol 44 ◽  
pp. 2-5
Author(s):  
W. Chiu ◽  
M.F. Schmid ◽  
T.-W. Jeng
Keyword(s):  
High Resolution ◽  
Fourier Transforms ◽  
Complex Structure ◽  
Distribution Functions ◽  
Multiple Image ◽  
Cryo Electron Microscopy ◽  
Structure Factors ◽  
Unit Cells ◽  
High Resolution Images ◽  
Phase Probability Distribution

Cryo-electron microscopy has been developed to the point where one can image thin protein crystals to 3.5 Å resolution. In our study of the crotoxin complex crystal, we can confirm this structural resolution from optical diffractograms of the low dose images. To retrieve high resolution phases from images, we have to include as many unit cells as possible in order to detect the weak signals in the Fourier transforms of the image. Hayward and Stroud proposed to superimpose multiple image areas by combining phase probability distribution functions for each reflection. The reliability of their phase determination was evaluated in terms of a crystallographic “figure of merit”. Grant and co-workers used a different procedure to enhance the signals from multiple image areas by vector summation of the complex structure factors in reciprocal space.

A large rotating structure around AB Doradus A at VLBI scale

2019 ◽  
Vol 15 (S354) ◽  
pp. 189-194
Author(s):  
J. B. Climent ◽  
J. C. Guirado ◽  
R. Azulay ◽  
J. M. Marcaide
Keyword(s):  
Magnetic Reconnection ◽  
Main Sequence ◽  
Complex Structure ◽  
Main Sequence Star ◽  
Polar Cap ◽  
Vlbi Observations ◽  
Rotating Structure ◽  
Source Structure ◽  
Expected Position

AbstractWe report the results of three VLBI observations of the pre-main-sequence star AB Doradus A at 8.4 GHz. With almost three years between consecutive observations, we found a complex structure at the expected position of this star for all epochs. Maps at epochs 2007 and 2010 show a double core-halo morphology while the 2013 map reveals three emission peaks with separations between 5 and 18 stellar radii. Furthermore, all maps show a clear variation of the source structure within the observing time. We consider a number of hypothesis in order to explain such observations, mainly: magnetic reconnection in loops on the polar cap, a more general loop scenario and a close companion to AB Dor A.

SAC3B is a target of CML19, the centrin 2 of Arabidopsis thaliana

2020 ◽  
Vol 477 (1) ◽  
pp. 173-189 ◽  
Author(s):  
Marco Pedretti ◽  
Carolina Conter ◽  
Paola Dominici ◽  
Alessandra Astegno
Keyword(s):  
Excision Repair ◽  
Complex Structure ◽  
Binding Motif ◽  
C Terminus ◽  
Repair Protein ◽  
Nucleotide Excision ◽  
Ef Hand ◽  
Molecular Determinants ◽  
Structure In Solution

Arabidopsis centrin 2, also known as calmodulin-like protein 19 (CML19), is a member of the EF-hand superfamily of calcium (Ca2+)-binding proteins. In addition to the notion that CML19 interacts with the nucleotide excision repair protein RAD4, CML19 was suggested to be a component of the transcription export complex 2 (TREX-2) by interacting with SAC3B. However, the molecular determinants of this interaction have remained largely unknown. Herein, we identified a CML19-binding site within the C-terminus of SAC3B and characterized the binding properties of the corresponding 26-residue peptide (SAC3Bp), which exhibits the hydrophobic triad centrin-binding motif in a reversed orientation (I8W4W1). Using a combination of spectroscopic and calorimetric experiments, we shed light on the SAC3Bp–CML19 complex structure in solution. We demonstrated that the peptide interacts not only with Ca2+-saturated CML19, but also with apo-CML19 to form a protein–peptide complex with a 1 : 1 stoichiometry. Both interactions involve hydrophobic and electrostatic contributions and include the burial of Trp residues of SAC3Bp. However, the peptide likely assumes different conformations upon binding to apo-CML19 or Ca2+-CML19. Importantly, the peptide dramatically increases the affinity for Ca2+ of CML19, especially of the C-lobe, suggesting that in vivo the protein would be Ca2+-saturated and bound to SAC3B even at resting Ca2+-levels. Our results, providing direct evidence that Arabidopsis SAC3B is a CML19 target and proposing that CML19 can bind to SAC3B through its C-lobe independent of a Ca2+ stimulus, support a functional role for these proteins in TREX-2 complex and mRNA export.

Crystal structures of Magnaporthe oryzae trehalose-6-phosphate synthase (MoTps1) suggest a model for catalytic process of Tps1

2019 ◽  
Vol 476 (21) ◽  
pp. 3227-3240 ◽  
Author(s):  
Shanshan Wang ◽  
Yanxiang Zhao ◽  
Long Yi ◽  
Minghe Shen ◽  
Chao Wang ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Conformational Changes ◽  
Magnaporthe Oryzae ◽  
Structural Information ◽  
Complex Structure ◽  
Critical Role ◽  
Catalytic Process ◽  
Structural Basis ◽  
Salt Bridges ◽  
Terminal Domain

Trehalose-6-phosphate (T6P) synthase (Tps1) catalyzes the formation of T6P from UDP-glucose (UDPG) (or GDPG, etc.) and glucose-6-phosphate (G6P), and structural basis of this process has not been well studied. MoTps1 (Magnaporthe oryzae Tps1) plays a critical role in carbon and nitrogen metabolism, but its structural information is unknown. Here we present the crystal structures of MoTps1 apo, binary (with UDPG) and ternary (with UDPG/G6P or UDP/T6P) complexes. MoTps1 consists of two modified Rossmann-fold domains and a catalytic center in-between. Unlike Escherichia coli OtsA (EcOtsA, the Tps1 of E. coli), MoTps1 exists as a mixture of monomer, dimer, and oligomer in solution. Inter-chain salt bridges, which are not fully conserved in EcOtsA, play primary roles in MoTps1 oligomerization. Binding of UDPG by MoTps1 C-terminal domain modifies the substrate pocket of MoTps1. In the MoTps1 ternary complex structure, UDP and T6P, the products of UDPG and G6P, are detected, and substantial conformational rearrangements of N-terminal domain, including structural reshuffling (β3–β4 loop to α0 helix) and movement of a ‘shift region' towards the catalytic centre, are observed. These conformational changes render MoTps1 to a ‘closed' state compared with its ‘open' state in apo or UDPG complex structures. By solving the EcOtsA apo structure, we confirmed that similar ligand binding induced conformational changes also exist in EcOtsA, although no structural reshuffling involved. Based on our research and previous studies, we present a model for the catalytic process of Tps1. Our research provides novel information on MoTps1, Tps1 family, and structure-based antifungal drug design.

A Structured Method for the Recognition of Complex Historical Tables

1997 ◽  
Vol 9 (1-3) ◽  
pp. 58-77
Author(s):  
Vitaly Kliatskine ◽  
Eugene Shchepin ◽  
Gunnar Thorvaldsen ◽  
Konstantin Zingerman ◽  
Valery Lazarev
Keyword(s):  
Nineteenth Century ◽  
Character Recognition ◽  
Optical Character Recognition ◽  
Complex Structure ◽  
Source Material ◽  
Historical Sources ◽  
Tax Assessment ◽  
Optical Character ◽  
Algorithmic Model ◽  
Machine Readable

In principle, printed source material should be made machine-readable with systems for Optical Character Recognition, rather than being typed once more. Offthe-shelf commercial OCR programs tend, however, to be inadequate for lists with a complex layout. The tax assessment lists that assess most nineteenth century farms in Norway, constitute one example among a series of valuable sources which can only be interpreted successfully with specially designed OCR software. This paper considers the problems involved in the recognition of material with a complex table structure, outlining a new algorithmic model based on ‘linked hierarchies’. Within the scope of this model, a variety of tables and layouts can be described and recognized. The ‘linked hierarchies’ model has been implemented in the ‘CRIPT’ OCR software system, which successfully reads tables with a complex structure from several different historical sources.

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