Acid–base effects, light emission, DNA-binding and photocleavage studies of oligo-homonuclear ruthenium(II) complexes and their computational study

2015 ◽  
Vol 432 ◽  
pp. 158-168 ◽  
Author(s):  
B. Senthamarai Kannan ◽  
D. Suresh Kumar ◽  
R. Host Antony David ◽  
A. Stalin ◽  
S. Ignacimuthu
Keyword(s):  
Dna Binding ◽  
Light Emission ◽  
Computational Study ◽  
Acid Base

Theoretical Studies of the Acid-Base Equilibria in a Model Active Site of the Human 20S Proteasome

2020 ◽  
Author(s):  
Jon Uranga ◽  
Lukas Hasecke ◽  
Jonny Proppe ◽  
Jan Fingerhut ◽  
Ricardo A. Mata
Keyword(s):  
Active Site ◽  
Boronic Acid ◽  
Computational Study ◽  
Ubiquitin Proteasome System ◽  
Bayesian Optimization ◽  
Inhibition Mechanism ◽  
20S Proteasome ◽  
Acid Base ◽  
Ubiquitin Proteasome ◽  
Infection Cycles

The 20S Proteasome is a macromolecule responsible for the chemical step in the ubiquitin-proteasome system of degrading unnecessary and unused proteins of the cell. It plays a central role both in the rapid growth of cancer cells as well as in viral infection cycles. Herein, we present a computational study of the acid-base equilibria in an active site of the human proteasome, an aspect which is often neglected despite the crucial role protons play in the catalysis. As example substrates, we take the inhibition by epoxy and boronic acid containing warheads. We have combined cluster quantum mechanical calculations, replica exchange molecular dynamics and Bayesian optimization of non-bonded potential terms in the inhibitors. In relation to the latter, we propose an easily scalable approach to the reevaluation of non-bonded potentials making use of QM/MM dynamics information. Our results show that coupled acid-base equilibria need to be considered when modeling the inhibition mechanism. The coupling between a neighboring lysine and the reacting threonine is not affected by the presence of the inhibitor.

Acid–base properties and DNA-binding of water soluble N-confused porphyrins with cationic side-arms

2008 ◽  
Vol 6 (22) ◽  
pp. 4157 ◽  
Author(s):  
Yoshiya Ikawa ◽  
Shoji Moriyama ◽  
Hiroyuki Harada ◽  
Hiroyuki Furuta
Keyword(s):  
Dna Binding ◽  
Water Soluble ◽  
Acid Base ◽  
Base Properties

Synthesis, and Acid–Base and DNA-Binding Properties of a Thiophen-Appended Ruthenium Complex

2011 ◽  
Vol 64 (2) ◽  
pp. 206 ◽  
Author(s):  
Hong Luo ◽  
Zhi-Ping Wang ◽  
An-Guo Zhang ◽  
Ke-Zhi Wang
Keyword(s):  
Dna Binding ◽  
Density Functional ◽  
Ruthenium Complex ◽  
Theoretical Calculations ◽  
Ionization Constants ◽  
Acid Base ◽  
Binding Properties ◽  
Emission Quenching ◽  
Melting Experiments ◽  
Dna Binding Properties

2-(5-Phenylthiophen-2-yl)-1H-imidazo[4,5-f][1,10]phenanthroline (Hptip) and its RuII complex [Ru(bpy)2(Hptip)](PF6)2 (where bpy = 2,2′-bipyridine) have been synthesized and characterized by elemental analysis, 1H NMR spectroscopy, and mass spectrometry. The acid–base properties of the complex were studied by UV-visible and luminescence spectrophotometric pH titrations, and ground- and excited-state acidity ionization constants were derived. The DNA-binding properties of [Ru(bpy)2(Hptip)](PF6)2 were also investigated by means of UV-vis and emission spectroscopy, salt effects, steady-state emission quenching by [Fe(CN)6]4–, DNA competitive binding with ethidium bromide, DNA melting experiments, and viscosity measurements. Density functional theoretical calculations were also carried out in order to understand the DNA binding properties.

scholarly journals Computational study of the effect of protonation states of PSA protein zinc fingers on its DNA binding

2019 ◽  
Vol 1274 ◽  
pp. 012002
Author(s):  
Nguyen Viet Duc ◽  
Ly Hai Nguyen ◽  
Hien T. T. Lai ◽  
Toan T. Nguyen
Keyword(s):  
Dna Binding ◽  
Computational Study ◽  
Zinc Fingers

Synthesis, characterization, computational study, DNA binding and molecular docking studies of chromium (III) drug-based complexes

2020 ◽  
Vol 1215 ◽  
pp. 128283 ◽  
Author(s):  
Saadullah G. Aziz ◽  
Shaaban A. Elroby ◽  
Abdesslem Jedidi ◽  
Bandar A. Babgi ◽  
Nujud S. Alshehri ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Dna Binding ◽  
Computational Study ◽  
Docking Studies ◽  
Molecular Docking Studies

scholarly journals Acidosis and Deafness in Patients with Recessive Mutations in FOXI1

2017 ◽  
Vol 29 (3) ◽  
pp. 1041-1048 ◽  
Author(s):  
Sven Enerbäck ◽  
Daniel Nilsson ◽  
Noel Edwards ◽  
Mikael Heglind ◽  
Sumaya Alkanderi ◽  
...  
Keyword(s):  
Dna Binding ◽  
Inner Ear ◽  
Renal Tubular Acidosis ◽  
Cultured Cells ◽  
Collecting Duct ◽  
Sensorineural Deafness ◽  
Distal Renal Tubular Acidosis ◽  
Acid Base ◽  
Recessive Mutations ◽  
Renal Tubular

Maintenance of the composition of inner ear fluid and regulation of electrolytes and acid-base homeostasis in the collecting duct system of the kidney require an overlapping set of membrane transport proteins regulated by the forkhead transcription factor FOXI1. In two unrelated consanguineous families, we identified three patients with novel homozygous missense mutations in FOXI1 (p.L146F and p.R213P) predicted to affect the highly conserved DNA binding domain. Patients presented with early-onset sensorineural deafness and distal renal tubular acidosis. In cultured cells, the mutations reduced the DNA binding affinity of FOXI1, which hence, failed to adequately activate genes crucial for normal inner ear function and acid-base regulation in the kidney. A substantial proportion of patients with a clinical diagnosis of inherited distal renal tubular acidosis has no identified causative mutations in currently known disease genes. Our data suggest that recessive mutations in FOXI1 can explain the disease in a subset of these patients.

scholarly journals Hetarylazopyrazolone Dyes Based on Benzothiazole and Benzimidazole Ring Systems: Synthesis, Spectroscopic Investigation, and Computational Study

2017 ◽  
Vol 2017 ◽  
pp. 1-10 ◽  
Author(s):  
Ebru Aktan ◽  
Tahsin Uyar
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Computational Study ◽  
Benzimidazole Ring ◽  
Acid Base ◽  
Functional Theory ◽  
Ring Systems ◽  
Td Dft ◽  
Elemental Analyses ◽  
Experimental Values

In this study, the synthesized coupling component 1-(2-benzothiazolyl)-3-methylpyrazol-5-one reacted with diazotised heterocyclic amines to afford six novel hetarylazopyrazolone dyes. These azo dyes based on benzothiazole and benzimidazole ring systems were characterized by spectral methods and elemental analyses. The solvatochromic behaviors of these dyes in various solvents were evaluated. The ground state geometries of the dyes were optimized using density functional theory (DFT). Solvent, acid-base, and substituent influences on the wavelength of the maximum absorption were examined in detail. Time-dependent density functional theory (TD-DFT) calculations were performed to obtain the absorption spectra of the dyes in various solvents and the results compared with experimental values. Besides, frontier molecular orbitals (FMO) analysis for the dyes is also described from the computational process.

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