DNase I – DNA interaction alters DNA and protein conformations

2008 ◽  
Vol 86 (3) ◽  
pp. 244-250 ◽  
Author(s):  
C.N. N’soukpoé-Kossi ◽  
S. Diamantoglou ◽  
H.A. Tajmir-Riahi
Keyword(s):  
Binding Constant ◽  
Protein Secondary Structure ◽  
Binding Mode ◽  
Dna Interaction ◽  
Minor Groove ◽  
Dnase I ◽  
Protein Conformations ◽  
Physiological Conditions ◽  
Α Helix ◽  
The Right

Human DNase I is an endonuclease that catalyzes the hydrolysis of double-stranded DNA predominantly by a single-stranded nicking mechanism under physiological conditions in the presence of divalent Mg and Ca cations. It binds to the minor groove and the backbone phosphate group and has no contact with the major groove of the right-handed DNA duplex. The aim of this study was to examine the effects of DNase I – DNA complexation on DNA and protein conformations.We monitored the interaction of DNA with DNase I under physiological conditions in the absence of Mg2+, with a constant DNA concentration (12.5 mmol/L; phosphate) and various protein concentrations (10–250 µmol/L). We used Fourier transfrom infrared, UV-visible, and circular dichroism spectroscopic methods to determine the protein binding mode, binding constant, and effects of polynucleotide–enzyme interactions on both DNA and protein conformations. Structural analyses showed major DNase–PO2 binding and minor groove interaction, with an overall binding constant, K, of 5.7 × 105 ± 0.78 × 105 (mol/L)–1. We found that the DNase I – DNA interaction altered protein secondary structure, with a major reduction in α helix and an increase in β sheet and random structures, and that a partial B-to-A DNA conformational change occurred. No DNA digestion was observed upon protein–DNA complexation.

The effect of aspirin-HSA complexation on the protein secondary structure

2000 ◽  
Vol 78 (2) ◽  
pp. 291-296 ◽  
Author(s):  
J F Neault ◽  
A Novetta-Delen ◽  
H Arakawa ◽  
H Malonga ◽  
H A Tajmir-Riahi
Keyword(s):  
Secondary Structure ◽  
Binding Constant ◽  
Structural Changes ◽  
Resolution Enhancement ◽  
Protein Secondary Structure ◽  
Binding Mode ◽  
Drug Binding ◽  
Drug Concentrations ◽  
Fitting Procedures ◽  
Α Helix

This study was designed to determine the secondary structure of human serum albumin (HSA) in the presence of aspirin in H2O and D2O solutions at physiological pH, using aspirin concentrations of 0.0001-5 mM with final protein concentration of 2% w/v. UV-vis spectra and Fourier transform infrared (FTIR) difference spectroscopy with its self-deconvolution, second derivative resolution enhancement, and curve-fitting procedures were applied to characterize the drug binding mode, the binding constant, and the protein secondary structure in the aspirin-HSA complexes. Spectroscopic evidence showed that no aspirin-protein interaction occurs at very low drug concentration (0.0001 mM), whereas at higher drug contents (0.001-0.1 mM) the aspirin anion binding (H-bonding) is mainly through the ε-amino NH3+ group with overall binding constant of K = 1.4 × 104 M-1. At high drug concentrations (1-5 mM), acetylation of Lys-199 was observed. Aspirin binding results in protein secondary structural changes from that of the α-helix 55% (free HSA) to 49%, β-sheet 22% (free HSA) to 31%, β-anti 12% (free HSA) to 4% and turn 11% (free HSA) to 16% in the aspirin-HSA complexes..Key words: aspirin, protein, drug, binding mode, binding constant secondary structure, FTIR spectroscopy.

scholarly journals The interaction of clenbuterol hydrochloride with bovine hemoglobin using spectroscopic techniques and molecular modeling methods

2009 ◽  
Vol 23 (5-6) ◽  
pp. 271-279 ◽  
Author(s):  
Yun Wu ◽  
Hui Mao ◽  
Bo Zhao ◽  
Jian Shen
Keyword(s):  
Molecular Modeling ◽  
Protein Secondary Structure ◽  
Binding Mode ◽  
Bovine Hemoglobin ◽  
Spectroscopic Techniques ◽  
Electronic Interaction ◽  
Physiological Conditions ◽  
Modeling Methods ◽  
Clenbuterol Hydrochloride ◽  
Hoff Equation

The interaction of clenbuterol hydrochloride (CL) to bovine hemoglobin (BHb) under physiological conditions was investigated by using UV-vis absorption, fluorescence, circular dichroism (CD) and molecular modeling. The fluorescence intensity of BHb decreased regularly with the gradual increasing concentration of CL. It is observed that there was a prominent interaction between CL and BHb. The fluorescence data revealed that the fluorescence quenching is a static process, and the thermodynamic parameters were calculated according to the Van't Hoff equation. The alternations of protein secondary structure in the presence of CL were determined by the evidence of CD. Molecular modeling study that corroborate our experimental results revealed that the binding mode of CL–BHb complex could be attributed to the hydrophobic interaction and hydrogen bonding, but electronic interaction cannot be excluded.

scholarly journals Interaction of thiacloprid with bovine hemoglobin using spectroscopic and molecular modeling methods

2010 ◽  
Vol 24 (5) ◽  
pp. 559-566
Author(s):  
Chang-Yun Chen ◽  
Bo Zhao ◽  
Zheng-Wu Wang
Keyword(s):  
Hydrogen Bonding ◽  
Molecular Modeling ◽  
Protein Secondary Structure ◽  
Binding Constants ◽  
Entropy Change ◽  
Binding Mode ◽  
Cd Spectroscopy ◽  
Bovine Hemoglobin ◽  
Standard Entropy ◽  
Α Helix

The interaction of thiacloprid (TL) to bovine hemoglobin (BHb) under physiological conditions was investigated by using fluorescence spectroscopy, circular dichroism spectroscopy (CD) and molecular modeling. The fluorescence intensity of BHb decreased regularly with the gradual increasing concentration of TL. It is observed that there was a prominent interaction between TL and BHb. The binding constantsKAat 288, 298 and 308 K obtained are 8.04, 5.26 and 3.08×104l · mol–1, respectively. The standard enthalpy change (ΔH°) and the standard entropy change (ΔS°) are calculated to be –34.54 KJ · mol–1and –25.77 J · mol–1 · K–1, which indicated that hydrogen bonding forces play major role in the interaction between TL and BHb. The alternations of protein secondary structure in the presence of TL were determined by CD spectroscopy. The results revealed that the content of α-helix was decreased from 51.85% in free BHb to 48.14% in TL–BHb complex. Molecular modeling study and our experimental results both showed that the binding mode of TL–BHb complex could be attributed to hydrogen bonding and hydrophobic interaction.

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.

scholarly journals DNA/BSA Binding, Molecular Docking, Nuclease Activity and Cytotoxicity Studies of Hydrazide Based Schiff Base Complexes

2019 ◽  
Vol 31 (12) ◽  
pp. 2941-2954
Author(s):  
Muthiah Chinnasamy ◽  
Andy Ramu
Keyword(s):  
Schiff Base ◽  
Molecular Docking ◽  
Metal Complexes ◽  
Binding Constant ◽  
Nuclease Activity ◽  
Binding Mode ◽  
Dna Interaction ◽  
Schiff Base Complexes ◽  
Spectral Techniques ◽  
Cytotoxicity Studies

A new series of hydrazide based Schiff base metal Cu(II)/Zn(II) complexes of the type [Cu(L1-L4)2] and [Zn(L1-L4)2] has been synthesized and characterized by various analytical and spectral techniques. The proposed geometry of metal complexes, square planar for Cu2+ ion and tetrahedral for Zn2+ ion was confirmed by the spectral and analytical results. DNA interaction with metal complexes was explored by spectral and molecular docking analysis. The results obtained indicates that Cu(II)/Zn(II) complexes interaction with DNA via an intercalative binding mode and its respective intrinsic binding constant (Kb) was found in the order of 7 > 8 > 5 > 6 > 3 > 4 > 1 > 2. Further, similar interactions of these metal complexes with BSA were found in the same order of binding constant. Furthermore, the complexes showed moderate cleavage ability with pUC19 DNA. Cytotoxicity studies confirmed the biological importance of the Schiff base complexes.

scholarly journals Structural and Technological Approach to Reveal the Role of the Lipid Phase in the Formation of Soy Emulsion Gels with Chia Oil

Gels ◽  
2021 ◽  
Vol 7 (2) ◽  
pp. 48
Author(s):  
Ana M. Herrero ◽  
Claudia Ruiz-Capillas
Keyword(s):  
Raman Spectroscopy ◽  
Structural Properties ◽  
Structural Changes ◽  
Protein Secondary Structure ◽  
Lipid Phase ◽  
Α Helix ◽  
Β Sheet ◽  
Shed Light ◽  
Chia Oil

Considerable attention has been paid to emulsion gels (EGs) in recent years due to their interesting applications in food. The aim of this work is to shed light on the role played by chia oil in the technological and structural properties of EGs made from soy protein isolates (SPI) and alginate. Two systems were studied: oil-free SPI gels (SPI/G) and the corresponding SPI EGs (SPI/EG) that contain chia oil. The proximate composition, technological properties (syneresis, pH, color and texture) and structural properties using Raman spectroscopy were determined for SPI/G and SPI/EG. No noticeable (p > 0.05) syneresis was observed in either sample. The pH values were similar (p > 0.05) for SPI/G and SPI/EG, but their texture and color differed significantly depending on the presence of chia oil. SPI/EG featured significantly lower redness and more lightness and yellowness and exhibited greater puncture and gel strengths than SPI/G. Raman spectroscopy revealed significant changes in the protein secondary structure, i.e., higher (p < 0.05) α-helix and lower (p < 0.05) β-sheet, turn and unordered structures, after the incorporation of chia oil to form the corresponding SPI/EG. Apparently, there is a correlation between these structural changes and the textural modifications observed.

scholarly journals Exploring aromatic cage flexibility of the histone methyllysine reader protein Spindlin1 and its impact on binding mode prediction: an in silico study

2021 ◽  
Author(s):  
Chiara Luise ◽  
Dina Robaa ◽  
Wolfgang Sippl
Keyword(s):  
Molecular Dynamic ◽  
In Silico ◽  
Binding Pocket ◽  
Binding Mode ◽  
Molecular Dynamic Simulations ◽  
Flexible Docking ◽  
Dynamic Simulations ◽  
Binding Mode Prediction ◽  
Aromatic Cage ◽  
The Right

AbstractSome of the main challenges faced in drug discovery are pocket flexibility and binding mode prediction. In this work, we explored the aromatic cage flexibility of the histone methyllysine reader protein Spindlin1 and its impact on binding mode prediction by means of in silico approaches. We first investigated the Spindlin1 aromatic cage plasticity by analyzing the available crystal structures and through molecular dynamic simulations. Then we assessed the ability of rigid docking and flexible docking to rightly reproduce the binding mode of a known ligand into Spindlin1, as an example of a reader protein displaying flexibility in the binding pocket. The ability of induced fit docking was further probed to test if the right ligand binding mode could be obtained through flexible docking regardless of the initial protein conformation. Finally, the stability of generated docking poses was verified by molecular dynamic simulations. Accurate binding mode prediction was obtained showing that the herein reported approach is a highly promising combination of in silico methods able to rightly predict the binding mode of small molecule ligands in flexible binding pockets, such as those observed in some reader proteins.

The clpB gene of Bifidobacterium breve UCC 2003: transcriptional analysis and first insights into stress induction

Microbiology ◽  
2005 ◽  
Vol 151 (9) ◽  
pp. 2861-2872 ◽  
Author(s):  
Marco Ventura ◽  
John G. Kenny ◽  
Ziding Zhang ◽  
Gerald F. Fitzgerald ◽  
Douwe van Sinderen
Keyword(s):  
3D Structure ◽  
Binding Mode ◽  
Dna Interaction ◽  
Transcriptional Analysis ◽  
Amino Acid Residues ◽  
Mobility Shift ◽  
Bifidobacterium Breve ◽  
Gel Mobility Shift ◽  
Slot Blot Analysis

The so-called clp genes, which encode components of the Clp proteolytic complex, are widespread among bacteria. The Bifidobacterium breve UCC 2003 genome contains a clpB gene with significant homology to predicted clpB genes from other members of the Actinobacteridae group. The heat- and osmotic-inducibility of the B. breve UCC 2003 clpB homologue was verified by slot-blot analysis, while Northern blot and primer extension analyses showed that the clpB gene is transcribed as a monocistronic unit with a single promoter. The role of a hspR homologue, known to control the regulation of clpB and dnaK gene expression in other high G+C content bacteria was investigated by gel mobility shift assays. Moreover the predicted 3D structure of HspR provides further insight into the binding mode of this protein to the clpB promoter region, and highlights the key amino acid residues believed to be involved in the protein–DNA interaction.

Catalytic properties of plate-like cadmium oxide nanoparticles in removal of sulfathiazole with anticancer activity

2018 ◽  
Vol 41 (3-4) ◽  
pp. 121-128 ◽  
Author(s):  
Leila Hoseini ◽  
Azar Bagheri
Keyword(s):  
Binding Constant ◽  
Cadmium Oxide ◽  
Reaction Times ◽  
Dna Interaction ◽  
New Drugs ◽  
Binding Modes ◽  
Hyperchromic Effect ◽  
Initial Ph ◽  
Ft Ir ◽  
Spectroscopy Studies

Abstract The study of the interaction of drugs with DNA is very exciting and significant not only for understanding the mechanism of the interaction but also for the design of new drugs. Here, we report the results of Fourier transform infrared (FT-IR) and ultraviolet (UV)-visible spectroscopy studies to determine the external binding modes of sulfathiazole (STZ), and the binding constant and stability of the STZ-DNA complex in aqueous solution. The results of absorption spectra showed that the interaction of STZ-DNA is weak because there is only a hyperchromic effect. A hyperchromic effect reflects the corresponding changes of DNA in its conformation and structure after the drug-DNA interaction has occurred. Spectroscopic evidence revealed that STZ binds DNA with an overall binding constant of K (STZ-DNA)=0.42×103 m−1. FT-IR spectroscopy showed that the complexation of STZ with DNA occurred via A-T and PO2 groups. Nano cadmium hydroxide has been synthesized using hexamine as the template at room temperature. Then, this nano cadmium hydroxide recrystallizes into nano cadmium oxide (CdO) at 400°C for 2 h. The product was characterized by using X-ray diffraction and scanning electron microscopy. The presence of drugs in aquatic media has emerged in the last decade as a new environmental risk. The other aim of this study was to investigate the degradation of the STZ antibiotic by nanosized CdO under ultraviolet irradiation. Various experimental parameters, such as initial CdO concentration, initial pH, and reaction times, were investigated. According to the results, this method has a good performance in the removal of STZ.

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