scholarly journals Joint neutron/X-ray crystal structure of a mechanistically relevant complex of perdeuterated urate oxidase and simulations provide insight into the hydration step of catalysis

IUCrJ ◽  
2021 ◽  
Vol 8 (1) ◽  
pp. 46-59
Author(s):  
Lindsay McGregor ◽  
Tamás Földes ◽  
Soi Bui ◽  
Martine Moulin ◽  
Nicolas Coquelle ◽  
...  
Keyword(s):  
Room Temperature ◽  
Crystallographic Analysis ◽  
Organic Substrate ◽  
Urate Oxidase ◽  
Nucleophilic Attack ◽  
Strong Hydrogen Bond ◽  
X Ray ◽  
Proton Relay ◽  
Dynamics Simulations ◽  
Peroxo Intermediate

Cofactor-independent urate oxidase (UOX) is an ∼137 kDa tetrameric enzyme essential for uric acid (UA) catabolism in many organisms. UA is first oxidized by O2 to dehydroisourate (DHU) via a peroxo intermediate. DHU then undergoes hydration to 5-hydroxyisourate (5HIU). At different stages of the reaction both catalytic O2 and water occupy the `peroxo hole' above the organic substrate. Here, high-resolution neutron/X-ray crystallographic analysis at room temperature has been integrated with molecular dynamics simulations to investigate the hydration step of the reaction. The joint neutron/X-ray structure of perdeuterated Aspergillus flavus UOX in complex with its 8-azaxanthine (8AZA) inhibitor shows that the catalytic water molecule (W1) is present in the peroxo hole as neutral H2O, oriented at 45° with respect to the ligand. It is stabilized by Thr57 and Asn254 on different UOX protomers as well as by an O—H...π interaction with 8AZA. The active site Lys10–Thr57 dyad features a charged Lys10–NH3 + side chain engaged in a strong hydrogen bond with Thr57OG1, while the Thr57OG1–HG1 bond is rotationally dynamic and oriented toward the π system of the ligand, on average. Our analysis offers support for a mechanism in which W1 performs a nucleophilic attack on DHUC5 with Thr57HG1 central to a Lys10-assisted proton-relay system. Room-temperature crystallography and simulations also reveal conformational heterogeneity for Asn254 that modulates W1 stability in the peroxo hole. This is proposed to be an active mechanism to facilitate W1/O2 exchange during catalysis.

A Novel Alkali-Metal Hydrido-tris(pyrazolyl)borate (Tp*) Complex. Isolation and Crystal Structure of [(Me2CO)3(NaTp*)2]

2014 ◽  
Vol 69 (7) ◽  
pp. 793-798
Author(s):  
Laurent Plasseraud ◽  
Hélène Cattey
Keyword(s):  
Crystal Structure ◽  
Alkali Metal ◽  
Sodium Hydroxide ◽  
Title Compound ◽  
Room Temperature ◽  
Crystallographic Analysis ◽  
Monoclinic Space Group ◽  
Large Excess ◽  
X Ray ◽  
Acetone Water

The title compound was isolated from the treatment of Tp*Sn(Cl)2Bu (1) with a large excess of sodium hydroxide in a mixture of acetone-water at room temperature. [(Me2CO)3(NaTp*)2] (2) crystallizes at 4 °C as prismatic colorless crystals, in the monoclinic space group P21/c with Z = 4, a = 12.2837(6), b = 24.3197(12), c = 16.9547(8) Å, β = 110.017(1)°, and V = 4759.0(4) Å3. The X-ray crystallographic analysis revealed a dinuclear unit in which two Tp*Na moieties are held together by three bridging acetone molecules acting as oxygen-based donors.

DFT Study on Two Plausible Mechanistic Routes to Pyrazolo[3,4-d]pyrimidine-4- Amines from Pyrazoloformimidate

2020 ◽  
Vol 24 (2) ◽  
pp. 216-229
Author(s):  
Amal Al-Azmi
Keyword(s):  
Density Functional ◽  
Room Temperature ◽  
Dft Calculation ◽  
Reaction Pathways ◽  
Nucleophilic Attack ◽  
X Ray Diffraction ◽  
Dimroth Rearrangement ◽  
Functional Theory ◽  
X Ray ◽  
Moderate Yield

Pyrazolo[3,4-d]pyrimidine-4-amine was prepared at room temperature in a catalyst- free medium with moderate yield and characterized by spectroscopic and X-ray diffraction techniques. Two possible mechanistic routes were suggested for its formation. Route 1 entails attack by the N of the amine on the imidate carbon followed by Dimroth rearrangement after cyclization. Route 2 is the nucleophilic attack by the amine on the CN function followed by cyclization to pyrazolo[3,4-d]pyrimidine-4-amine. Density functional theory (DFT) calculation studies of the two proposed reaction pathways illustrated that the Route 2 reaction was more likely than that of Route 1.

3-(4-Bromobenzoyl)-N-phenyl-1,3-oxazolidin-2-imine

2006 ◽  
Vol 62 (4) ◽  
pp. o1306-o1307
Author(s):  
Taek Hyeon Kim ◽  
Jung Hee Jang ◽  
Uk Lee
Keyword(s):  
Title Compound ◽  
Room Temperature ◽  
Crystallographic Analysis ◽  
X Ray ◽  
Compound C

The title compound, C17H15BrN2O2, was prepared by the reaction of 2-anilino-4-methyl-2-oxazoline with 4-bromobenzoyl chloride in the presence of potassium tert-butoxide at room temperature. X-ray crystallographic analysis shows that the endo-substituted product is formed.

scholarly journals Molecular lock regulates binding of glycine to a primitive NMDA receptor

2016 ◽  
Vol 113 (44) ◽  
pp. E6786-E6795 ◽  
Author(s):  
Alvin Yu ◽  
Robert Alberstein ◽  
Alecia Thomas ◽  
Austin Zimmet ◽  
Richard Grey ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Biochemical Analysis ◽  
Salt Bridge ◽  
Binding Pocket ◽  
Crystallographic Analysis ◽  
Mnemiopsis Leidyi ◽  
X Ray ◽  
Ligand Affinity ◽  
Rate Of Recovery ◽  
Dynamics Simulations

The earliest metazoan ancestors of humans include the ctenophore Mnemiopsis leidyi. The genome of this comb jelly encodes homologs of vertebrate ionotropic glutamate receptors (iGluRs) that are distantly related to glycine-activated NMDA receptors and that bind glycine with unusually high affinity. Using ligand-binding domain (LBD) mutants for electrophysiological analysis, we demonstrate that perturbing a ctenophore-specific interdomain Arg-Glu salt bridge that is notably absent from vertebrate AMPA, kainate, and NMDA iGluRs greatly increases the rate of recovery from desensitization, while biochemical analysis reveals a large decrease in affinity for glycine. X-ray crystallographic analysis details rearrangements in the binding pocket stemming from the mutations, and molecular dynamics simulations suggest that the interdomain salt bridge acts as a steric barrier regulating ligand binding and that the free energy required to access open conformations in the glycine-bound LBD is largely responsible for differences in ligand affinity among the LBD variants.

Crystallization and preliminary X-ray crystallographic analysis of archaeal O 6-methylguanine–DNA methyltransferase

1998 ◽  
Vol 54 (6) ◽  
pp. 1395-1396 ◽  
Author(s):  
Hiroshi Hashimoto ◽  
Motomu Nishioka ◽  
Tsuyoshi Inoue ◽  
Shinsuke Fujiwara ◽  
Masahiro Takagi ◽  
...  
Keyword(s):  
Dna Methyltransferase ◽  
Room Temperature ◽  
Crystallographic Analysis ◽  
X Ray Diffraction ◽  
X Ray ◽  
Methylguanine Dna Methyltransferase ◽  
Protein Mass ◽  
Cell Dimensions ◽  
Unit Cell Dimensions ◽  
Crystal Volume

Crystals of archaeal O 6-methylguanine–DNA methyltransferase (MGMT) from hyperthermophilic archaeon Pyrococcus kodakaraensis strain KOD1 have been grown at room temperature using polyethylene glycol as a precipitant. The diffraction pattern of the crystal extends to 2.0 Å resolution at room temperature upon exposure to Cu K\alpha radiation. The crystal belongs to the space group P212121 with unit-cell dimensions of a = 52.8, b = 86.6 and c = 39.9 Å. The presence of one molecule per asymmetric unit gives a crystal volume per protein mass (Vm ) of 2.3 Å3 Da−1 and a solvent content of 48% by volume. A full set of X-ray diffraction data was collected to 2.0 Å Bragg spacings from the native crystal.

Preliminary X-ray crystallographic analysis of Bowman–Birk trypsin inhibitor from barley seeds

1998 ◽  
Vol 54 (3) ◽  
pp. 441-443 ◽  
Author(s):  
Hyun Kyu Song ◽  
Se Won Suh
Keyword(s):  
Trypsin Inhibitor ◽  
Room Temperature ◽  
Crystallographic Analysis ◽  
X Rays ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Protein Mass ◽  
Crystal Volume

Bowman–Birk trypsin inhibitor from barley seeds has been crystallized at room temperature using polyethylene glycol as precipitant. The crystal is tetragonal, belonging to the space group P41212 (or P43212), with unit cell parameters of a = b = 62.48 and c = 94.63 Å. The asymmetric unit contains one molecule of Bowman–Birk trypsin inhibitor with corresponding crystal volume per protein mass (Vm ) of 2.89 Å3 Da−1 and the solvent content of 57% by volume. The crystals diffract to at least 1.9 Å Bragg spacing upon exposure to synchrotron X-rays. X-ray data to 1.9 Å have been collected from a native crystal.

Comparison of the Structure of Liquid Amides as Determined by Diffraction Experiments and Molecular Dynamics Simulations

1995 ◽  
Vol 50 (1) ◽  
pp. 38-50 ◽  
Author(s):  
Pia C. Schoester ◽  
Manfred D. Zeidler ◽  
Tamäs Radnai ◽  
Philippe A. Bopp
Keyword(s):  
Molecular Dynamics ◽  
Room Temperature ◽  
Heavy Atom ◽  
Distribution Functions ◽  
X Ray ◽  
Atom Pairs ◽  
Dynamics Simulations ◽  
Pair Distribution Functions ◽  
Flexible Models ◽  
Site Pair

The intermodular structures of liquid formamide, N-methylformamide and N,N-dimethylformamide at room temperature are studied by means of NVE molecular dynamics computer simulations. Newly developed flexible models are used. X-ray and neutron weighted structure and total radial pair distribution functions are computed from the simulated site-site pair distribution functions. They are compared with experimental results. The agreement is usually satisfactory as far as heavy atom pairs are concerned while the lengths of the hydrogen bonds are found to be systematically too long in the simulations.

Thieme Chemistry Journals Awardees – Where Are They Now? Bis(2-pyridyl)amides as Readily Cleavable Amides Under Catalytic, Neutral, and Room-Temperature Conditions

Synlett ◽  
2017 ◽  
Vol 29 (03) ◽  
pp. 301-305 ◽  
Author(s):  
Naoya Kumagai ◽  
Masakatsu Shibasaki ◽  
Shinya Adachi
Keyword(s):  
Driving Force ◽  
Room Temperature ◽  
Metal Cations ◽  
Crystallographic Analysis ◽  
Metal Coordination ◽  
Acid Base ◽  
X Ray ◽  
Temperature Conditions

Mild solvolytic cleavage of bis(2-pyridyl)amide under neutral and room-temperature conditions is described. The inherently stable amide was readily activated by catalytic amounts of metal cations to react with alcohols. Based on X-ray crystallographic analysis, the primary driving force was considered to be amide distortion induced by the metal coordination of two pyridyl groups in a bidentate fashion without affecting the amide functionality. The compatibility of the acid/base-sensitive functionalities and the absence of racemization during solvolysis highlight the mildness of the present protocol.

Crystallization and preliminary X-ray crystallographic analysis of a vancomycin–N-acetyl-D-Ala-D-Ala complex

1999 ◽  
Vol 55 (2) ◽  
pp. 534-535 ◽  
Author(s):  
Deborah McPhail ◽  
Alan Cooper ◽  
Andy Freer
Keyword(s):  
Room Temperature ◽  
Crystallographic Analysis ◽  
Diffusion Method ◽  
The Novel ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
Solvent Content ◽  
X Ray ◽  
Cell Parameters ◽  
Crystal Density

A vancomycin–N-acetyl-D-Ala-D-Ala complex has been crystallized by the sitting-drop vapour-diffusion method using imidazole maleic buffer at pH 7.6. The novel crystals obtained belong to the space group P6322 with unit-cell parameters a = b = 73.43 (1), c = 277.17 (4) Å, γ = 120°. The crystal density was determined as 1.106 g cm−3 which gives a supercell of 24 molecules (12 dimers) per asymmetric unit for an acceptable Matthews number and an estimated solvent content of 42%. Data were collected at room temperature to 2.8 Å.

Sign in / Sign up

Export Citation Format

Share Document