scholarly journals Structural analysis of protein–DNA and protein–RNA interactions by FTIR, UV-visible and CD spectroscopic methods

2009 ◽  
Vol 23 (2) ◽  
pp. 81-101 ◽  
Author(s):  
H. A. Tajmir-Riahi ◽  
C. N. N'soukpoé-Kossi ◽  
D. Joly
Keyword(s):  
Binding Sites ◽  
Ribonuclease A ◽  
Rnase A ◽  
Fundamental Question ◽  
Spectroscopic Methods ◽  
Deoxyribonuclease I ◽  
Calf Thymus ◽  
Uv Visible ◽  
Rna Interaction ◽  
Structural Aspects

In this chapter the fundamental question of how does protein–DNA or protein–RNA interaction affect the structures and dynamics of DNA, RNA and protein is addressed. Models for calf-thymus DNA and transfer RNA interactions with human serum albumin (HSA), ribonuclease A (RNase A) and deoxyribonuclease I (DNase I) are presented here, using Fourier Transform Infrared (FTIR) spectroscopy in conjunction with UV-visible and CD spectroscopic methods. In the models considered, the binding sites, stability and structural aspects of protein–DNA and protein–RNA are discussed and the effects of protein interaction on the secondary structures of DNA, RNA and protein were determined.

RNase A – tRNA binding alters protein conformation

2007 ◽  
Vol 85 (3) ◽  
pp. 311-318 ◽  
Author(s):  
C.N. N’soukpoé-Kossi ◽  
C. Ragi ◽  
H.A. Tajmir-Riahi
Keyword(s):  
Binding Sites ◽  
Binding Constant ◽  
Structural Changes ◽  
Structural Information ◽  
Binding Mode ◽  
Rnase A ◽  
Random Coil ◽  
Pancreatic Ribonuclease A ◽  
Α Helix ◽  
Rna Interaction

Bovine pancreatic ribonuclease A (RNase A) catalyzes the cleavage of P-O5′ bonds in RNA on the 3′ side of pyrimidine to form cyclic 2′,5′-phosphates. Even though extensive structural information is available on RNase A complexes with mononucleotides and oligonucleotides, the interaction of RNase A with tRNA has not been fully investigated. We report the complexation of tRNA with RNase A in aqueous solution under physiological conditions, using a constant RNA concentration and various amounts of RNase A. Fourier transform infrared, UV-visible, and circular dichroism spectroscopic methods were used to determine the RNase binding mode, binding constant, sequence preference, and biopolymer secondary structural changes in the RNase–tRNA complexes. Spectroscopic results showed 2 major binding sites for RNase A on tRNA, with an overall binding constant of K = 4.0 × 105 (mol/L)–1. The 2 binding sites were located at the G-C base pairs and the backbone PO2 group. Protein–RNA interaction alters RNase secondary structure, with a major reduction in α helix and β sheets and an increase in the turn and random coil structures, while tRNA remains in the A conformation upon protein interaction. No tRNA digestion was observed upon RNase A complexation.

Investigation of Some Characterizations of Black TiO\(_2\) Nanotubes Via Spectroscopic Methods

2019 ◽  
Vol 29 (2) ◽  
pp. 189 ◽  
Author(s):  
Tho Truong Nguyen ◽  
Thi Minh Cao ◽  
Hieu Van Le ◽  
Viet Van Pham
Keyword(s):  
Water Splitting ◽  
Oxygen Vacancies ◽  
Light Response ◽  
Nanotube Arrays ◽  
Spectroscopic Methods ◽  
Visible Light Response ◽  
Uv Visible ◽  
Visible Reflectance ◽  
Splitting Effect ◽  
Anodization Method

The black TiO\(_2\) with substantial Ti\(^3+\) and oxygen vacancies exhibit an excellent photoelectrochemical water-splitting performance due to the improved charge transport the extended visible light response. In this study, black TiO\(_2\) nanotube arrays synthesized by the anodization method, and then, they have been investigated some characterizations by spectroscopic methods such as UV-visible reflectance (UV-vis DRS), Fourier-transform infrared spectroscopy (FTIR), Raman spectroscopy, and photoluminescence spectrum. The results showed that some highlighted properties of the black TiO2 nanotube arrays and they could apply for water-splitting effect.

scholarly journals Overcoming the design, build, test bottleneck for synthesis of nonrepetitive protein-RNA cassettes

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Noa Katz ◽  
Eitamar Tripto ◽  
Naor Granik ◽  
Sarah Goldberg ◽  
Orna Atar ◽  
...  
Keyword(s):  
Binding Site ◽  
Binding Sites ◽  
Mammalian Cells ◽  
Coat Proteins ◽  
Structural Determinants ◽  
Design Build ◽  
Machine Learning Approach ◽  
Successful Design ◽  
Experimental Findings ◽  
Rna Interaction

AbstractWe apply an oligo-library and machine learning-approach to characterize the sequence and structural determinants of binding of the phage coat proteins (CPs) of bacteriophages MS2 (MCP), PP7 (PCP), and Qβ (QCP) to RNA. Using the oligo library, we generate thousands of candidate binding sites for each CP, and screen for binding using a high-throughput dose-response Sort-seq assay (iSort-seq). We then apply a neural network to expand this space of binding sites, which allowed us to identify the critical structural and sequence features for binding of each CP. To verify our model and experimental findings, we design several non-repetitive binding site cassettes and validate their functionality in mammalian cells. We find that the binding of each CP to RNA is characterized by a unique space of sequence and structural determinants, thus providing a more complete description of CP-RNA interaction as compared with previous low-throughput findings. Finally, based on the binding spaces we demonstrate a computational tool for the successful design and rapid synthesis of functional non-repetitive binding-site cassettes.

A Pyoverdin from the Antarctica Strain 51W of Pseudomonas fluorescens

1999 ◽  
Vol 54 (3-4) ◽  
pp. 156-162 ◽  
Author(s):  
Jessica Voss ◽  
Kambiz Taraz ◽  
Herbert Budzikiewicz
Keyword(s):  
Amino Acids ◽  
Pseudomonas Fluorescens ◽  
Binding Sites ◽  
Chemical Shifts ◽  
Chemical Degradation ◽  
Spectroscopic Methods ◽  
Extreme Conditions ◽  
Structural Elements ◽  
Nmr Data ◽  
Schirmacher Oasis

From the strain 51W of Pseudomonas fluorescens living under extreme conditions at the Schirmacher Oasis (Antarctica) a pyoverdin was obtained. Its structure was elucidated by chemical degradation and spectroscopic methods. The NMR data of the pyoverdin and of its Ga(III) complex were compared. Appreciable influences of the metal on the chemical shifts of the atoms at its binding sites were observed. Thus the structural elements involved in the complexation can be identified and coinciding signals of amino acids occurring more than once in the peptide chain can be separated.

Mapping the protein-binding sites for iridium(iii)-based CO-releasing molecules

2016 ◽  
Vol 45 (30) ◽  
pp. 12206-12214 ◽  
Author(s):  
Marco Caterino ◽  
Ariel A. Petruk ◽  
Alessandro Vergara ◽  
Giarita Ferraro ◽  
Daniela Marasco ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Protein Binding ◽  
Binding Sites ◽  
Raman Microspectroscopy ◽  
Rnase A ◽  
Protein Binding Sites ◽  
X Ray ◽  
X Ray Crystallography ◽  
Model Protein ◽  
Circular Dichroïsm

Mass spectrometry, Raman microspectroscopy, circular dichroism and X-ray crystallography have been used to investigate the reaction of CO-releasing molecule Cs2IrCl5CO with the model protein RNase A.

scholarly journals Some Metal Ions Complexes Derived From Schiff Base Ligand with Anthranillic Acid: Preparation, Spectroscopic and Biological Studies

2020 ◽  
Vol 17 (1) ◽  
pp. 0099
Author(s):  
Lekaa khalid Karem
Keyword(s):  
Schiff Base ◽  
Schiff Base Ligand ◽  
Magnetic Moment ◽  
Primary Amine ◽  
Molar Conductivity ◽  
Spectroscopic Methods ◽  
Geometrical Shape ◽  
Biological Studies ◽  
Different Types ◽  
Uv Visible

This search includes the preparation of Schiff base ligand (SB) from condensation primary amine with vanillin. The new ligand was diagnosed by spectroscopic methods as Mass, NMR, CHN and FTIR. Ligand complexes were mixed from new (SB) and Anthranillic acid (A) with five metal (II) chlorides. The preparation and diagnosis were conducted by FTIR, CHN, UV-visible, molar conductivity, atomic absorption and magnetic moment. The octahedral geometrical shape of the complexes was proposed. The ligands and their new complexes were screened with two different types of bacteria.

scholarly journals Effects of cross-linked dimers of ribonuclease A or of lysozyme on the processing of endocytosed peroxidase by hepatoma cells

1982 ◽  
Vol 202 (2) ◽  
pp. 543-550
Author(s):  
J Bartholeyns ◽  
P Baudhuin
Keyword(s):  
Mechanism Of Action ◽  
Binding Sites ◽  
Culture Medium ◽  
Basic Protein ◽  
Intracellular Localization ◽  
Ribonuclease A ◽  
Protein Processing ◽  
Intracellular Protein ◽  
Intracellular Degradation ◽  
Htc Cells

Cross-linked dimers of ribonuclease, added at a concentration of 0.05 mg/ml to the culture medium of hepatoma (HTC) cells, were previously shown to inhibit intracellular degradation of peroxidase taken up by endocytosis. Intracellular localization showed that endocytosed peroxidase does not reach lysosomes in dimer-treated cells. The present study shows that preloading of lysosomes with fluorescent anti-peroxidase IgG, obtained by exposing HTC cells for 48 h to 0.1 mg of antibody/ml, restores intracellular degradation of endocytosed peroxidase. Moreover, accumulation of peroxidase into lysosomes, which no longer occurs in dimer-treated cells, occurs again under these conditions. We conclude that inhibition of transfer of peroxidase from phagosomes to lysosomes is most likely to be the alteration resulting from the exposure of the cells to ribonuclease dimer, rather than inhibition of fusion between phagosomes and lysosomes. The dimer of another basic protein, lysozyme added at a concentration of 0.2 mg/ml to the culture medium, is shown to induce the same type of effects as does the dimer of ribonuclease; the half-life of endocytosed peroxidase increased from 5 to 15 h after 2 h exposure of HTC cells to dimerized lysozyme. The effect of both dimers on intracellular protein processing can be reversed by addition of 100 mm-galactose to the culture medium, up to 5 h after pretreatment of the cells. The dimers of ribonuclease A or of lysozyme have thus probably the same mechanism of action. Evidence that the two dimers share the same binding sites on the cells is presented.

scholarly journals PRIME-3D2D is a 3D2D model to predict binding sites of protein–RNA interaction

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Juan Xie ◽  
Jinfang Zheng ◽  
Xu Hong ◽  
Xiaoxue Tong ◽  
Shiyong Liu
Keyword(s):  
Full Advantage ◽  
High Throughput ◽  
Binding Sites ◽  
High Throughput Sequencing ◽  
Secondary Structures ◽  
Biological Processes ◽  
Genome Wide ◽  
Rna Interaction ◽  
Rna Complexes ◽  
Better Than

AbstractProtein-RNA interaction participates in many biological processes. So, studying protein–RNA interaction can help us to understand the function of protein and RNA. Although the protein–RNA 3D3D model, like PRIME, was useful in building 3D structural complexes, it can’t be used genome-wide, due to lacking RNA 3D structures. To take full advantage of RNA secondary structures revealed from high-throughput sequencing, we present PRIME-3D2D to predict binding sites of protein–RNA interaction. PRIME-3D2D is almost as good as PRIME at modeling protein–RNA complexes. PRIME-3D2D can be used to predict binding sites on PDB data (MCC = 0.75/0.70 for binding sites in protein/RNA) and transcription-wide (MCC = 0.285 for binding sites in RNA). Testing on PDB and yeast transcription-wide data show that PRIME-3D2D performs better than other binding sites predictor. So, PRIME-3D2D can be used to predict the binding sites both on PDB and genome-wide, and it’s freely available.

scholarly journals Link between Affinity and Cu(II) Binding Sites to Amyloid-β Peptides Evaluated by a New Water-Soluble UV–Visible Ratiometric Dye with a Moderate Cu(II) Affinity

2017 ◽  
Vol 89 (3) ◽  
pp. 2155-2162 ◽  
Author(s):  
Amandine Conte-Daban ◽  
Valentina Borghesani ◽  
Stéphanie Sayen ◽  
Emmanuel Guillon ◽  
Yves Journaux ◽  
...  
Keyword(s):  
Binding Sites ◽  
Amyloid Β ◽  
Water Soluble ◽  
Uv Visible
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