scholarly journals Calculation of the CD Spectrum of Class A β-Lactamase from Escherichia coli (TEM-1)

2001 ◽  
Vol 56 (11) ◽  
pp. 757-760 ◽  
Author(s):  
C. Christov ◽  
S. Gabriel ◽  
B. Atanasov ◽  
J. Fleischhauer
Keyword(s):  
Escherichia Coli ◽  
Matrix Method ◽  
Side Chain ◽  
Calculated Spectrum ◽  
X Ray Diffraction ◽  
Class A ◽  
Cd Spectrum ◽  
Diffraction Structure ◽  
The Matrix ◽  
Rotational Strengths

Abstract The Circular Dichroism (CD) spectrum of β-lactamase from Escherichia coli (TEM-1) has been calculated with the matrix method on the basis of the x-ray diffraction structure. All known transitions in the peptide and side-chain groups, especially the aromatic and disulfide groups have been included. The calculations were performed with and without the tryptophan (Trp) residues. Rotational strengths calculated with the matrix method were combined with Gaussians to generate the CD spectrum. The calculated spectrum reproduces the signs and approximate magnitudes of the CD bands rather w ell only when the trytophan side chains are included. However, the experimental negative double band at 208 and 222 nm, which is characteristic for a-helices, is absent in the calculated spectrum.

scholarly journals Bicyclic Boronates as Potent Inhibitors of AmpC, the Class C β-Lactamase from Escherichia coli

Biomolecules ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 899 ◽  
Author(s):  
Pauline A. Lang ◽  
Anete Parkova ◽  
Thomas M. Leissing ◽  
Karina Calvopiña ◽  
Ricky Cain ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Active Site ◽  
High Energy ◽  
Structural Basis ◽  
Side Chain ◽  
Class A ◽  
Dual Action ◽  
Class C ◽  
Tract Infections ◽  
Site Binding

Resistance to β-lactam antibacterials, importantly via production of β-lactamases, threatens their widespread use. Bicyclic boronates show promise as clinically useful, dual-action inhibitors of both serine- (SBL) and metallo- (MBL) β-lactamases. In combination with cefepime, the bicyclic boronate taniborbactam is in phase 3 clinical trials for treatment of complicated urinary tract infections. We report kinetic and crystallographic studies on the inhibition of AmpC, the class C β-lactamase from Escherichia coli, by bicyclic boronates, including taniborbactam, with different C-3 side chains. The combined studies reveal that an acylamino side chain is not essential for potent AmpC inhibition by active site binding bicyclic boronates. The tricyclic form of taniborbactam was observed bound to the surface of crystalline AmpC, but not at the active site, where the bicyclic form was observed. Structural comparisons reveal insights into why active site binding of a tricyclic form has been observed with the NDM-1 MBL, but not with other studied β-lactamases. Together with reported studies on the structural basis of inhibition of class A, B and D β-lactamases, our data support the proposal that bicyclic boronates are broad-spectrum β-lactamase inhibitors that work by mimicking a high energy ‘tetrahedral’ intermediate. These results suggest further SAR guided development could improve the breadth of clinically useful β-lactamase inhibition.

scholarly journals Matrix Method for X-Ray Stress Measurement in Single Crystals, and the Rational Planning of the Measurements

2014 ◽  
Vol 996 ◽  
pp. 58-63
Author(s):  
Balder Ortner
Keyword(s):  
Single Crystals ◽  
Matrix Method ◽  
Stress Measurement ◽  
X Ray Diffraction ◽  
X Ray ◽  
Stress Calculation ◽  
Rational Planning ◽  
The Matrix ◽  
Experimental Effort

With the so-called matrix method stress calculation from x-ray diffraction measurements is much easier than it used to be with older methods. The matrix method is also well suited to optimize the choice of reflections (hkl) to be measured in order to obtain the best results with least experimental effort. Pseudocodes for the stress calculation are given.

Isomorphous replacement in electron diffraction of wet crystals of rat hemoglobin

1983 ◽  
Vol 41 ◽  
pp. 446-447
Author(s):  
William F. Tivol ◽  
Murray Vernon King ◽  
D. F. Parsons
Keyword(s):  
Electron Diffraction ◽  
Heavy Atom ◽  
Isomorphous Substitution ◽  
X Ray Diffraction ◽  
Salt Solutions ◽  
X Ray ◽  
Isomorphous Replacement ◽  
Structure Factors ◽  
Diffraction Structure ◽  
The Mean

Feasibility of isomorphous substitution in electron diffraction is supported by a calculation of the mean alteration of the electron-diffraction structure factors for hemoglobin crystals caused by substituting two mercury atoms per molecule, following Green, Ingram & Perutz, but with allowance for the proportionality of f to Z3/4 for electron diffraction. This yields a mean net change in F of 12.5%, as contrasted with 22.8% for x-ray diffraction.Use of the hydration chamber in electron diffraction opens prospects for examining many proteins that yield only very thin crystals not suitable for x-ray diffraction. Examination in the wet state avoids treatments that could cause translocation of the heavy-atom labels or distortion of the crystal. Combined with low-fluence techniques, it enables study of the protein in a state as close to native as possible.We have undertaken a study of crystals of rat hemoglobin by electron diffraction in the wet state. Rat hemoglobin offers a certain advantage for hydration-chamber work over other hemoglobins in that it can be crystallized from distilled water instead of salt solutions.

scholarly journals Optical, Structural, and Dielectric Properties of Composites Based on Thermoplastic Polymers of the Polyolefin and Polyurethane Type and BaTiO3 Nanoparticles

Materials ◽  
2021 ◽  
Vol 14 (4) ◽  
pp. 753
Author(s):  
M. Baibarac ◽  
A. Nila ◽  
I. Smaranda ◽  
M. Stroe ◽  
L. Stingescu ◽  
...  
Keyword(s):  
Crystallization Process ◽  
Weight Ratio ◽  
Thermoplastic Elastomers ◽  
Visible Spectral Range ◽  
X Ray Diffraction ◽  
Thermoplastic Polymers ◽  
The Matrix ◽  
Free Films ◽  
Batio3 Nanoparticles ◽  
Properties Of Composites

In this work, new films containing composite materials based on blends of thermoplastic polymers of the polyurethane (TPU) and polyolefin (TPO) type, in the absence and presence of BaTiO3 nanoparticles (NPs) with the size smaller 100 nm, were prepared. The vibrational properties of the free films depending on the weight ratio of the two thermoplastic polymers were studied. Our results demonstrate that these films are optically active, with strong, broad, and adjustable photoluminescence by varying the amount of TPU. The crystalline structure of BaTiO3 and the influence of thermoplastic polymers on the crystallization process of these inorganic NPs were determined by X-ray diffraction (XRD) studies. The vibrational changes induced in the thermoplastic polymer’s matrix of the BaTiO3 NPs were showcased by Raman scattering and FTIR spectroscopy. The incorporation of BaTiO3 NPs in the matrix of thermoplastic elastomers revealed the shift dependence of the photoluminescence (PL) band depending on the BaTiO3 NP concentration, which was capable of covering a wide visible spectral range. The dependencies of the dielectric relaxation phenomena with the weight of BaTiO3 NPs in thermoplastic polymers blends were also demonstrated.

scholarly journals “Newton’s cradle” proton relay with amide–imidic acid tautomerization in inverting cellulase visualized by neutron crystallography

2015 ◽  
Vol 1 (7) ◽  
pp. e1500263 ◽  
Author(s):  
Akihiko Nakamura ◽  
Takuya Ishida ◽  
Katsuhiro Kusaka ◽  
Taro Yamada ◽  
Shinya Fushinobu ◽  
...  
Keyword(s):  
Glycoside Hydrolases ◽  
Side Chain ◽  
Enzymatic Reactions ◽  
X Ray Diffraction ◽  
Peptide Bonds ◽  
Proton Relay ◽  
Newton’S Cradle ◽  
Dynamics Simulations ◽  
Hydrolysis Of

Hydrolysis of carbohydrates is a major bioreaction in nature, catalyzed by glycoside hydrolases (GHs). We used neutron diffraction and high-resolution x-ray diffraction analyses to investigate the hydrogen bond network in inverting cellulase PcCel45A, which is an endoglucanase belonging to subfamily C of GH family 45, isolated from the basidiomycete Phanerochaete chrysosporium. Examination of the enzyme and enzyme-ligand structures indicates a key role of multiple tautomerizations of asparagine residues and peptide bonds, which are finally connected to the other catalytic residue via typical side-chain hydrogen bonds, in forming the “Newton’s cradle”–like proton relay pathway of the catalytic cycle. Amide–imidic acid tautomerization of asparagine has not been taken into account in recent molecular dynamics simulations of not only cellulases but also general enzyme catalysis, and it may be necessary to reconsider our interpretation of many enzymatic reactions.

scholarly journals Binding Site of the Bridged Macrolides in the Escherichia coli Ribosome

2005 ◽  
Vol 49 (1) ◽  
pp. 281-288 ◽  
Author(s):  
Liqun Xiong ◽  
Yakov Korkhin ◽  
Alexander S. Mankin
Keyword(s):  
Escherichia Coli ◽  
Tight Binding ◽  
Dimethyl Sulfate ◽  
23S Rrna ◽  
Side Chain ◽  
Macrolide Antibiotics ◽  
Side Chains ◽  
Alkyl Aryl ◽  
E Coli ◽  
Exit Tunnel

ABSTRACT Ketolides represent the latest group of macrolide antibiotics. Tight binding of ketolides to the ribosome appears to correlate with the presence of an extended alkyl-aryl side chain. Recently developed 6,11-bridged bicyclic ketolides extend the spectrum of platforms used to generate new potent macrolides with extended alkyl-aryl side chains. The purpose of the present study was to characterize the site of binding and the action of bridged macrolides in the ribosomes of Escherichia coli. All the bridged macrolides investigated efficiently protected A2058 and A2059 in domain V of 23S rRNA from modification by dimethyl sulfate and U2609 from modification by carbodiimide. In addition, bridged macrolides that carry extended alkyl-aryl side chains protruding from the 6,11 bridge protected A752 in helix 35 of domain II of 23S rRNA from modification by dimethyl sulfate. Bridged macrolides efficiently displaced erythromycin from the ribosome in a competition binding assay. The A2058G mutation in 23S rRNA conferred resistance to the bridged macrolides. The U2609C mutation, which renders E. coli resistant to the previously studied ketolides telithromycin and cethromycin, barely affected cell susceptibility to the bridged macrolides used in this study. The results of the biochemical and genetic studies indicate that in the E. coli ribosome, bridged macrolides bind in the nascent peptide exit tunnel at the site previously described for other macrolide antibiotics. The presence of the side chain promotes the formation of specific interactions with the helix 35 of 23S rRNA.

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