Bioorganometallic Chemistry. 27. Synthetic, X-ray Crystallographic, and Competitive Binding Studies in the Reactions of Nucleobases, Nucleosides, and Nucleotides with [Cp*Rh(H2O)3](OTf)2, as a Function of pH, and the Utilization of Several Cp*Rh–DNA Base Complexes in Host–Guest Chemistry

2014 ◽  
Vol 33 (10) ◽  
pp. 2389-2404 ◽  
Author(s):  
David P. Smith ◽  
Hong Chen ◽  
Seiji Ogo ◽  
Ana I. Elduque ◽  
Miriam Eisenstein ◽  
...  
Keyword(s):  
Competitive Binding ◽  
Binding Studies ◽  
X Ray ◽  
Bioorganometallic Chemistry ◽  
Dna Base ◽  
Guest Chemistry

Renal angiotensin II receptors and protein kinase C in diabetic rats: effects of insulin and ACE inhibition

2000 ◽  
Vol 278 (4) ◽  
pp. F603-F612 ◽  
Author(s):  
Farhad Amiri ◽  
Raul Garcia
Keyword(s):  
Protein Kinase C ◽  
Protein Kinase ◽  
Ace Inhibition ◽  
Treated Group ◽  
Diabetic Rats ◽  
Competitive Binding ◽  
Ang Ii ◽  
Binding Studies ◽  
Kinase C ◽  
High Insulin

It has been shown that glomerular ANG II receptors are downregulated and protein kinase C (PKC) activity is enhanced in diabetes mellitus. Therefore, we investigated glomerular and preglomerular vascular ANG II receptors and PKC isoform regulation in streptozotocin (STZ)-diabetic rats treated with insulin and/or captopril. Diabetic rats were prepared by injecting STZ (60 mg/kg). Those that developed diabetes after 48 h were treated with low or high doses of insulin, or with a low dose of insulin as well as captopril, and killed 14 days later. Their glomeruli and preglomerular vessels were purified, competitive binding studies were performed by using the ANG II antagonists losartan and PD-123319, and PKC analysis was carried out by Western blotting. Competitive binding studies showed that the AT1 receptor was the only ANG II receptor detected on both glomeruli and preglomerular vessels of all groups. Preglomerular vascular AT1 receptor density (Bmax) was significantly upregulated in low insulin-treated STZ rats, whereas glomerular AT1 Bmax was downregulated. Furthermore, both the captopril- and high insulin-treated groups had less glomerulosclerosis and vascular damage than the low insulin-treated group. PKCα, PKCδ, PKCε, and PKCμ isoforms found in preglomerular vessels were upregulated by captopril and high insulin doses, respectively, whereas no such regulation occurred in glomeruli. We conclude that in STZ-diabetic rats ANG II receptors and PKC isoforms on preglomerular vessels and glomeruli are differentially regulated by treatment with insulin and/or captopril.

scholarly journals Comparative binding of bovine, human and rat insulin-like growth factors to membrane receptors and to antibodies against human insulin-like growth factor-1

1986 ◽  
Vol 233 (1) ◽  
pp. 215-221 ◽  
Author(s):  
L C Read ◽  
F J Ballard ◽  
G L Francis ◽  
R C Baxter ◽  
C J Bagley ◽  
...  
Keyword(s):  
Growth Factors ◽  
Polyclonal Antiserum ◽  
Competitive Binding ◽  
Membrane Receptors ◽  
Binding Studies ◽  
Comparative Binding ◽  
Placental Membranes ◽  
Insulin Like Growth Factors

The immunological properties of human, bovine and rat insulin-like growth factors (IGF) and insulin were compared in competitive binding studies with Tr10 and NPA polyclonal antisera raised in rabbits against human IGF-1. Bovine IGF-1 was 11-19% as effective as human IGF-1 in competing for binding with 125I-labelled human IGF-1, whereas IGF-2 reacted poorly and insulin did not compete. Similar competitive binding curves were obtained with the mouse monoclonal anti-(human IGF-1) antibody 3D1, except that bovine IGF-1 showed a severalfold greater affinity for the monoclonal antibody than for either polyclonal antiserum. Membranes isolated from human placenta, sheep placenta and foetal-human liver were used as sources of cellular receptors. In human placental membranes, most of the binding of IGF-1 tracers could be attributed to a type-1 receptor, because insulin inhibited up to 65% of tracer binding. The other two tissues apparently contain only type-2 receptors, as evidenced by the very low potency of bovine or human IGF-1 in competing for binding with IGF-2 tracers and the absence of any competition by insulin. In competition for binding with labelled bovine or human IGF-1 to human placental membranes, bovine IGF-1 had a similar potency to human IGF-1, whereas bovine IGF-1 was more potent in binding studies with tissues rich in type-2 receptors. Rat IGF-2 was considerably less effective than human IGF-2 in competition for receptors on any of the membrane preparations.

scholarly journals Dynamic oligopeptide acquisition by the RagAB transporter from Porphyromonas gingivalis

2019 ◽  
Author(s):  
Mariusz Madej ◽  
Joshua B. R. White ◽  
Zuzanna Nowakowska ◽  
Shaun Rawson ◽  
Carsten Scavenius ◽  
...  
Keyword(s):  
Porphyromonas Gingivalis ◽  
Direct Evidence ◽  
Inflammatory Diseases ◽  
Extracellular Proteins ◽  
Substrate Selectivity ◽  
Binding Studies ◽  
Uptake Mechanism ◽  
X Ray ◽  
Cryo Electron Microscopy ◽  
Binding Surface

AbstractPorphyromonas gingivalis, an asaccharolytic Bacteroidetes, is a keystone pathogen in human periodontitis that may also contribute to the development of other chronic inflammatory diseases, such as rheumatoid arthritis, cardiovascular disease and Alzheimer’s disease. P. gingivalis utilizes protease-generated peptides derived from extracellular proteins for growth, but how those peptides enter the cell is not clear. Here we identify RagAB as the outer membrane importer for peptides. X-ray crystal structures show that the transporter forms a dimeric RagA2B2 complex with the RagB substrate binding surface-anchored lipoprotein forming a closed lid on the TonB-dependent transporter RagA. Cryo-electron microscopy structures reveal the opening of the RagB lid and thus provide direct evidence for a “pedal bin” nutrient uptake mechanism. Together with mutagenesis, peptide binding studies and RagAB peptidomics, our work identifies RagAB as a dynamic OM oligopeptide acquisition machine with considerable substrate selectivity that is essential for the efficient utilisation of proteinaceous nutrients by P. gingivalis.

scholarly journals NSLS-II MX beamlines FMX for micro-crystallography & AMX for highly automated MX

2014 ◽  
Vol 70 (a1) ◽  
pp. C1733-C1733
Author(s):  
Martin Fuchs ◽  
Robert Sweet ◽  
Lonny Berman ◽  
Dileep Bhogadi ◽  
Wayne Hendrickson ◽  
...  
Keyword(s):  
Energy Range ◽  
Structure Determination ◽  
Optical Systems ◽  
Photon Flux ◽  
X Rays ◽  
Macromolecular Crystallography ◽  
Binding Studies ◽  
X Ray ◽  
Array Detectors ◽  
Broad Energy Range

We present the final design of the x-ray optical systems and experimental stations of the two macromolecular crystallography (MX) beamlines, FMX and AMX, at the National Synchrotron Light Source-II (NSLS-II). Along with its companion x-ray scattering beamline, LIX, this suite of Advanced Beamlines for Biological Investigations with X-rays (ABBIX, [1]) will begin user operation in 2016. The pair of MX beamlines with complementary and overlapping capabilities is located at canted undulators (IVU21) in sector 17-ID. The Frontier Microfocusing Macromolecular Crystallography beamline (FMX) will deliver a photon flux of ~5x10^12 ph/s at a wavelength of 1 Å into a spot of 1 - 50 µm size. It will cover a broad energy range from 5 - 30 keV, corresponding to wavelengths from 0.4 - 2.5 Å. The highly Automated Macromolecular Crystallography beamline (AMX) will be optimized for high throughput applications, with beam sizes from 4 - 100 µm, an energy range of 5 - 18 keV (0.7 - 2.5 Å), and a flux at 1 Å of ~10^13 ph/s. Central components of the in-house-developed experimental stations are a 100 nm sphere of confusion goniometer with a horizontal axis, piezo-slits to provide dynamic beam size changes during diffraction experiments, a dedicated secondary goniometer for crystallization plates, and sample- and plate-changing robots. FMX and AMX will support a broad range of biomedical structure determination methods from serial crystallography on micron-sized crystals, to structure determination of complexes in large unit cells, to rapid sample screening and data collection of crystals in trays, for instance to characterize membrane protein crystals and to conduct ligand-binding studies. Together with the solution scattering program at LIX, the new beamlines will offer unique opportunities for advanced diffraction experiments with micro- and mini-beams, with next generation hybrid pixel array detectors and emerging crystal delivery methods such as acoustic droplet ejection. This work is supported by the US National Institutes of Health.

IN VITRO DNA BINDING STUDIES OF SELECTED HETEROCYCLIC COMPOUNDS

INDIAN DRUGS ◽  
2018 ◽  
Vol 55 (12) ◽  
pp. 24-26
Author(s):  
C Akhila ◽  
◽  
P Lalitha
Keyword(s):  
Dna Binding ◽  
Heterocyclic Compounds ◽  
Uv Spectroscopy ◽  
Binding Mode ◽  
Spectroscopic Technique ◽  
Binding Studies ◽  
Base Pairs ◽  
Dna Base ◽  
Dna Binding Studies

DNA binding studies of selected heterocyclic compounds belonging to the class of quinolinones, substituted quinolinones and thiones were carried out using ct-DNA. The binding nature of the compounds with DNA analyzed using UV-spectroscopy revealed the compounds to be DNA intercalators demonstrating the binding nature of compounds with DNA base pairs. This study is aimed at establishing a facile UV spectroscopic technique to arrive at the binding mode of DNA to ligands.

scholarly journals Probing the Role of Divalent Metal Ions in a Bacterial Psychrophilic Metalloprotease: Binding Studies of an Enzyme in the Crystalline State by X-Ray Crystallography

2003 ◽  
Vol 185 (14) ◽  
pp. 4195-4203 ◽  
Author(s):  
Stephanie Ravaud ◽  
Patrice Gouet ◽  
Richard Haser ◽  
Nushin Aghajari
Keyword(s):  
Metal Ions ◽  
Calcium Ions ◽  
Calcium Ion ◽  
Crystalline State ◽  
Zinc Ion ◽  
Binding Studies ◽  
X Ray ◽  
X Ray Crystallography ◽  
Catalytic Zinc

ABSTRACT The psychrophilic alkaline metalloprotease (PAP) produced by a Pseudomonas bacterium isolated in Antarctica belongs to the clan of metzincins, for which a zinc ion is essential for catalytic activity. Binding studies in the crystalline state have been performed by X-ray crystallography in order to improve the understanding of the role of the zinc and calcium ions bound to this protease. Cocrystallization and soaking experiments with EDTA in a concentration range from 1 to 85 mM have resulted in five three-dimensional structures with a distinct number of metal ions occupying the ion-binding sites. Evolution of the structural changes observed in the vicinity of each cation-binding site has been studied as a function of the concentration of EDTA, as well as of time, in the presence of the chelator. Among others, we have found that the catalytic zinc ion was the first ion to be chelated, ahead of a weakly bound calcium ion (Ca 700) exclusive to the psychrophilic enzyme. Upon removal of the catalytic zinc ion, the side chains of the active-site residues His-173, His-179 and Tyr-209 shifted ∼4, 1.0, and 1.6 Å, respectively. Our studies confirm and also explain the sensitivity of PAP toward moderate EDTA concentrations and propose distinct roles for the calcium ions. A new crystal form of native PAP validates our previous predictions regarding the adaptation of this enzyme to cold environments as well as the proteolytic domain calcium ion being exclusive for PAP independent of crystallization conditions.

scholarly journals Structural basis of nucleoside and nucleoside drug selectivity by concentrative nucleoside transporters

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Zachary Lee Johnson ◽  
Jun-Ho Lee ◽  
Kiyoun Lee ◽  
Minhee Lee ◽  
Do-Yeon Kwon ◽  
...  
Keyword(s):  
Antiviral Agents ◽  
Nucleoside Transporters ◽  
Structural Basis ◽  
Biological Processes ◽  
Functional Information ◽  
Binding Studies ◽  
X Ray ◽  
Equilibrium Binding ◽  
Drug Selectivity ◽  
Proof Of Principle

Concentrative nucleoside transporters (CNTs) are responsible for cellular entry of nucleosides, which serve as precursors to nucleic acids and act as signaling molecules. CNTs also play a crucial role in the uptake of nucleoside-derived drugs, including anticancer and antiviral agents. Understanding how CNTs recognize and import their substrates could not only lead to a better understanding of nucleoside-related biological processes but also the design of nucleoside-derived drugs that can better reach their targets. Here, we present a combination of X-ray crystallographic and equilibrium-binding studies probing the molecular origins of nucleoside and nucleoside drug selectivity of a CNT from Vibrio cholerae. We then used this information in chemically modifying an anticancer drug so that it is better transported by and selective for a single human CNT subtype. This work provides proof of principle for utilizing transporter structural and functional information for the design of compounds that enter cells more efficiently and selectively.

scholarly journals Gentle, fast and effective crystal soaking by acoustic dispensing

2017 ◽  
Vol 73 (3) ◽  
pp. 246-255 ◽  
Author(s):  
Patrick M. Collins ◽  
Jia Tsing Ng ◽  
Romain Talon ◽  
Karolina Nekrosiute ◽  
Tobias Krojer ◽  
...  
Keyword(s):  
High Throughput ◽  
Solvent Tolerance ◽  
X Ray Diffraction ◽  
Binding Studies ◽  
Structure Based Drug Design ◽  
X Ray ◽  
Active Structure ◽  
Droplet Ejection ◽  
Lysine Demethylase ◽  
Positional Precision

The steady expansion in the capacity of modern beamlines for high-throughput data collection, enabled by increasing X-ray brightness, capacity of robotics and detector speeds, has pushed the bottleneck upstream towards sample preparation. Even in ligand-binding studies using crystal soaking, the experiment best able to exploit beamline capacity, a primary limitation is the need for gentle and nontrivial soaking regimens such as stepwise concentration increases, even for robust and well characterized crystals. Here, the use of acoustic droplet ejection for the soaking of protein crystals with small molecules is described, and it is shown that it is both gentle on crystals and allows very high throughput, with 1000 unique soaks easily performed in under 10 min. In addition to having very low compound consumption (tens of nanolitres per sample), the positional precision of acoustic droplet ejection enables the targeted placement of the compound/solvent away from crystals and towards drop edges, allowing gradual diffusion of solvent across the drop. This ensures both an improvement in the reproducibility of X-ray diffraction and increased solvent tolerance of the crystals, thus enabling higher effective compound-soaking concentrations. The technique is detailed here with examples from the protein target JMJD2D, a histone lysine demethylase with roles in cancer and the focus of active structure-based drug-design efforts.

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