scholarly journals Structure of Human Cyclophilin A in Complex with the Novel Immunosuppressant Sanglifehrin A at 1.6 Å Resolution

2005 ◽  
Vol 280 (23) ◽  
pp. 21965-21971 ◽  
Author(s):  
Joerg Kallen ◽  
Richard Sedrani ◽  
Gerhard Zenke ◽  
Juergen Wagner
Keyword(s):  
Crystal Structure ◽  
Three Dimensional ◽  
Cyclophilin A ◽  
The Other ◽  
Size Exclusion ◽  
Dimensional Structure ◽  
The Novel ◽  
Immunosuppressive Activity ◽  
Exclusion Chromatography ◽  
Sanglifehrin A

Sanglifehrin A (SFA) is a novel immunosuppressant isolated from Streptomyces sp. that binds strongly to the human immunophilin cyclophilin A (CypA). SFA exerts its immunosuppressive activity through a mode of action different from that of all other known immunophilin-binding substances, namely cyclosporine A (CsA), FK506, and rapamycin. We have determined the crystal structure of human CypA in complex with SFA at 1.6 Å resolution. The high resolution of the structure revealed the absolute configuration at all 17 chiral centers of SFA as well as the details of the CypA/SFA interactions. In particular, it was shown that the 22-membered macrocycle of SFA is deeply embedded in the same binding site as CsA and forms six direct hydrogen bonds with CypA. The effector domain of SFA, on the other hand, has a chemical and three-dimensional structure very different from CsA, already strongly suggesting different immunosuppressive mechanisms. Furthermore, two CypA·SFA complexes form a dimer in the crystal as well as in solution as shown by light scattering and size exclusion chromatography experiments. This observation raises the possibility that the dimer of CypA·SFA complexes is the molecular species mediating the immunosuppressive effect.

A new three-dimensional anionic cadmium(II) dicyanamide network

2014 ◽  
Vol 70 (11) ◽  
pp. 1054-1056 ◽  
Author(s):  
Qiang Li ◽  
Hui-Ting Wang
Keyword(s):  
Crystal Structure ◽  
Aqueous Solution ◽  
Unit Cell Volume ◽  
Three Dimensional ◽  
Building Blocks ◽  
The Other ◽  
Dimensional Structure ◽  
Cadmium Nitrate ◽  
Nitrate Tetrahydrate ◽  
Anionic Framework

A new cadmium dicyanamide complex, poly[tetramethylphosphonium [μ-chlorido-di-μ-dicyanamido-κ4N1:N5-cadmium(II)]], [(CH3)4P][Cd(NCNCN)2Cl], was synthesized by the reaction of tetramethylphosphonium chloride, cadmium nitrate tetrahydrate and sodium dicyanamide in aqueous solution. In the crystal structure, each CdIIatom is octahedrally coordinated by four terminal N atoms from four anionic dicyanamide (dca) ligands and by two chloride ligands. The dicyanamide ligands play two different roles in the building up of the structure; one role results in the formation of [Cd(dca)Cl]2building blocks, while the other links the building blocks into a three-dimensional structure. The anionic framework exhibits a solvent-accessible void of 673.8 Å3, amounting to 47.44% of the total unit-cell volume. The cavities in the network are occupied by pairs of tetramethylphosphonium cations.

scholarly journals trans-Bis(2,2′-bipyridine-4,4′-dicarboxylic acid-κ2 N,N′)dichloridoruthenium(III) perchlorate

IUCrData ◽  
2018 ◽  
Vol 3 (11) ◽  
Author(s):  
Lívia Gonçalves Leida Soares ◽  
Diego Silva Padilha ◽  
Roberto Salgado Amado ◽  
Marciela Scarpellini
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Carboxylic Acid ◽  
Dicarboxylic Acid ◽  
Three Dimensional ◽  
The Other ◽  
Dimensional Structure ◽  
Hydrogen Bonding Interactions ◽  
Octahedral Environment ◽  
Small Distortion

In the crystal structure of the ruthenium(III) complex, trans-[RuIII(dcbpy)2Cl2]ClO4 (dcbpy = 2,2′-bipyridine-4,4′-dicarboxylic acid, C12H8N2O4), the RuIII atom lies on an inversion centre, showing a small distortion in its octahedral environment. The Ru—Cl bond lengths are shorter than those present in the analogous trans-ruthenium(II) compound containing the bipyridine ligand. The C—O distances in the two symmetry-independent carboxylic acid moieties of the ligand are similar in one group, but different in the other. This is probably due to the different intermolecular interactions they experience with neighbouring cationic complexes. The hydrogen-bonding interactions in which they are involved form a three-dimensional structure, similar to those found in coordination polymers.

scholarly journals Organophosphorus acid anhydrolase fromAlteromonas macleodii: structural study and functional relationship to prolidases

2013 ◽  
Vol 69 (4) ◽  
pp. 346-354 ◽  
Author(s):  
Andrea Štěpánková ◽  
Jarmila Dušková ◽  
Tereza Skálová ◽  
Jindřich Hašek ◽  
Tomáš Koval' ◽  
...  
Keyword(s):  
Active Site ◽  
Three Dimensional ◽  
Size Exclusion ◽  
Dimensional Structure ◽  
Cell Parameters ◽  
Bacterial Enzyme ◽  
Organophosphorus Acid Anhydrolase ◽  
Full Structure ◽  
Exclusion Chromatography ◽  
Pita Bread

The bacterial enzyme organophosphorus acid anhydrolase (OPAA) is able to catalyze the hydrolysis of both proline dipeptides (Xaa-Pro) and several types of organophosphate (OP) compounds. The full three-dimensional structure of the manganese-dependent OPAA enzyme is presented for the first time. This enzyme, which was originally isolated from the marine bacteriumAlteromonas macleodii, was prepared recombinantly inEscherichia coli. The crystal structure was determined at 1.8 Å resolution in space groupC2, with unit-cell parametersa= 133.8,b= 49.2,c= 97.3 Å, β = 125.0°. The enzyme forms dimers and their existence in solution was confirmed by dynamic light scattering and size-exclusion chromatography. The enzyme shares the pita-bread fold of its C-terminal domain with related prolidases. The binuclear manganese centre is located in the active site within the pita-bread domain. Moreover, an Ni2+ion from purification was localized according to anomalous signal. This study presents the full structure of this enzyme with complete surroundings of the active site and provides a critical analysis of its relationship to prolidases.

scholarly journals Ammonium imidazolium dichromate

2012 ◽  
Vol 68 (4) ◽  
pp. m389-m389 ◽  
Author(s):  
Run-Qiang Zhu
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Title Compound ◽  
Three Dimensional ◽  
The Other ◽  
Dimensional Structure ◽  
Compound C ◽  
The Mean ◽  
Anions And Cations ◽  
Dichromate Anions

In the crystal structure of the title compound, (C3H5N2)(NH4)[Cr2O7], the anions and cations are linked through N—H...O hydrogen bonds, resulting in a three-dimensional structure which contains three kinds of layers parallel to (001). One layer contains imidazole cations, the other two layers the ammonium cations and dichromate anions. The dichromate anion has an eclipsed conformation with a dihedral angle of 14.65 (18)° between the mean planes of the O—P—O—P—O backbone.

scholarly journals Hydrothermal Synthesis and Structural Investigation of a Crystalline Uranyl Borosilicate

Inorganics ◽  
2021 ◽  
Vol 9 (4) ◽  
pp. 25
Author(s):  
Kristen A. Pace ◽  
Vladislav V. Klepov ◽  
Mark D. Smith ◽  
Travis Williams ◽  
Gregory Morrison ◽  
...  
Keyword(s):  
Synthesis Method ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Exploratory Research ◽  
The Novel ◽  
Orthorhombic Space Group ◽  
Crystalline Materials ◽  
Waste Remediation ◽  
And Storage ◽  
X Ray Absorption

The relevance of multidimensional and porous crystalline materials to nuclear waste remediation and storage applications has motivated exploratory research focused on materials discovery of compounds, such as actinide mixed-oxoanion phases, which exhibit rich structural chemistry. The novel phase K1.8Na1.2[(UO2)BSi4O12] has been synthesized using hydrothermal methods, representing the first example of a uranyl borosilicate. The three-dimensional structure crystallizes in the orthorhombic space group Cmce with lattice parameters a = 15.5471(19) Å, b = 14.3403(17) Å, c = 11.7315(15) Å, and V = 2615.5(6) Å3, and is composed of UO6 octahedra linked by [BSi4O12]5− chains to form a [(UO2)BSi4O12]3− framework. The synthesis method, structure, results of Raman, IR, and X-ray absorption spectroscopy, and thermal stability are discussed.

scholarly journals Nanofiber-Mâché Hollow Ball Mimicking the Three-Dimensional Structure of a Cyst

Polymers ◽  
2021 ◽  
Vol 13 (14) ◽  
pp. 2273
Author(s):  
Wan-Ying Huang ◽  
Norichika Hashimoto ◽  
Ryuhei Kitai ◽  
Shin-ichiro Suye ◽  
Satoshi Fujita
Keyword(s):  
Three Dimensional ◽  
Hollow Structure ◽  
Dimensional Structure ◽  
The Novel ◽  
Fibrous Scaffold ◽  
Hydrogel Beads ◽  
Inner Surface ◽  
Intracranial Epidermoid ◽  
Hollow Ball

The occasional malignant transformation of intracranial epidermoid cysts into squamous cell carcinomas remains poorly understood; the development of an in vitro cyst model is urgently needed. For this purpose, we designed a hollow nanofiber sphere, the “nanofiber-mâché ball.” This hollow structure was fabricated by electrospinning nanofiber onto alginate hydrogel beads followed by dissolving the beads. A ball with approximately 230 mm3 inner volume provided a fibrous geometry mimicking the topography of the extracellular matrix. Two ducts located on opposite sides provided a route to exchange nutrients and waste. This resulted in a concentration gradient that induced oriented migration, in which seeded cells adhered randomly to the inner surface, formed a highly oriented structure, and then secreted a dense web of collagen fibrils. Circumferentially aligned fibers on the internal interface between the duct and hollow ball inhibited cells from migrating out of the interior, similar to a fish bottle trap. This structure helped to form an adepithelial layer on the inner surface. The novel nanofiber-mâché technique, using a millimeter-sized hollow fibrous scaffold, is excellently suited to investigating cyst physiology.

The first crystal structure of the peptidase domain of the U32 peptidase family

2015 ◽  
Vol 71 (12) ◽  
pp. 2505-2512 ◽  
Author(s):  
Magdalena Schacherl ◽  
Angelika A. M. Montada ◽  
Elena Brunstein ◽  
Ulrich Baumann
Keyword(s):  
Crystal Structure ◽  
Catalytic Mechanism ◽  
Quaternary Structure ◽  
Catalytic Domain ◽  
Three Dimensional ◽  
Zinc Ion ◽  
Crystal Structure Analysis ◽  
Dimensional Structure ◽  
Sequence Motifs ◽  
Conserved Sequence

The U32 family is a collection of over 2500 annotated peptidases in the MEROPS database with unknown catalytic mechanism. They mainly occur in bacteria and archaea, but a few representatives have also been identified in eukarya. Many of the U32 members have been linked to pathogenicity, such as proteins fromHelicobacterandSalmonella. The first crystal structure analysis of a U32 catalytic domain fromMethanopyrus kandleri(genemk0906) reveals a modified (βα)8TIM-barrel fold with some unique features. The connecting segment between strands β7 and β8 is extended and helix α7 is located on top of the C-terminal end of the barrel body. The protein exhibits a dimeric quaternary structure in which a zinc ion is symmetrically bound by histidine and cysteine side chains from both monomers. These residues reside in conserved sequence motifs. No typical proteolytic motifs are discernible in the three-dimensional structure, and biochemical assays failed to demonstrate proteolytic activity. A tunnel in which an acetate ion is bound is located in the C-terminal part of the β-barrel. Two hydrophobic grooves lead to a tunnel at the C-terminal end of the barrel in which an acetate ion is bound. One of the grooves binds to aStrep-Tag II of another dimer in the crystal lattice. Thus, these grooves may be binding sites for hydrophobic peptides or other ligands.

scholarly journals Crystal structure of 2-benzylamino-4-(4-methoxyphenyl)-6,7,8,9-tetrahydro-5H-cyclohepta[b]pyridine-3-carbonitrile

2014 ◽  
Vol 70 (12) ◽  
pp. 525-527 ◽  
Author(s):  
R. A. Nagalakshmi ◽  
J. Suresh ◽  
S. Maharani ◽  
R. Ranjith Kumar ◽  
P. L. Nilantha Lakshman
Keyword(s):  
Crystal Structure ◽  
Pyridine Ring ◽  
Three Dimensional ◽  
Chair Conformation ◽  
Dimensional Structure ◽  
Compound C ◽  
Centroid Distance ◽  
Steric Crowding ◽  
Benzene Rings ◽  
Group A

The title compound, C25H25N3O, comprises a 2-aminopyridine ring fused with a cycloheptane ring, which adopts a chair conformation. The central pyridine ring (r.m.s. deviation = 0.013 Å) carries three substituents,viz.a benzylamino group, a methoxyphenyl ring and a carbonitrile group. The N atom of the carbonitrile group is significantly displaced [by 0.2247 (1) Å] from the plane of the pyridine ring, probably due to steric crowding involving the adjacent substituents. The phenyl and benzene rings are inclined to one another by 58.91 (7)° and to the pyridine ring by 76.68 (7) and 49.80 (6)°, respectively. In the crystal, inversion dimers linked by pairs of N—H...Nnitrilehydrogen bonds generateR22(14) loops. The dimers are linked by C—H...π and slipped parallel π–π interactions [centroid–centroid distance = 3.6532 (3) Å] into a three-dimensional structure.

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