MODELING THE CONCENTRATIONS AND EFFICIENCIES FOR THE INTERACTING SPECIES OF PYROPHEOPHORBIDE METHYL ESTER-COPPER ASSOCIATION

2013 ◽  
Vol 08 (01n02) ◽  
pp. 73-87 ◽  
Author(s):  
S. AL-OMARI
Keyword(s):  
Methyl Ester ◽  
Fluorescence Quenching ◽  
Binding Site ◽  
Binding Constant ◽  
Pharmacokinetics And Pharmacodynamics ◽  
Dynamic Binding ◽  
Binding Interaction ◽  
Interacting Species ◽  
Different Temperatures ◽  
Dynamic Fluorescence

The interaction between pyropheophorbide methyl ester (PPME) and Cu 2+ was investigated using UV-vis and fluorescence spectrscopy. Study of the binding interaction between PPME and Cu 2+ could contribute to understanding of its pharmacokinetics and pharmacodynamics. Parameters of the static and dynamic fluorescence quenching of PPME- Cu 2+ association were calculated at different temperatures. For binding site of 1:1 at 299 K, the static binding constant (kS), the static isosbestic concentration ([Formula: see text]), the dynamic binding constant (kD), and the dynamic isosbestic concentration ([Formula: see text]) are, respectively, 61 M-1, 0.0164 M, 75 M-1, and 0.0133 M. The concentrations and efficiencies of the intermediates species were modeled. Satisfactory correspondence between the experimental and calculated results was found.

Separation of static and dynamic thermodynamic parameters for the interaction between pyropheophorbide methyl ester and copper

2014 ◽  
Vol 18 (04) ◽  
pp. 297-304 ◽  
Author(s):  
Saleh Al-Omari
Keyword(s):  
Free Energy ◽  
Methyl Ester ◽  
Fluorescence Quenching ◽  
Thermodynamic Function ◽  
Binding Constant ◽  
Entropy Change ◽  
Enthalpy Change ◽  
Gibbs Free Energy Change ◽  
Quenching Process ◽  
Different Temperatures

The interaction between pyropheophorbide methyl ester (PPME) and the ionic metal of copper ( Cu 2+) was investigated using fluorescence and UV-vis techniques. By analysis of the fluorescence spectra, it was observed that Cu 2+ has a strong ability to quench the intrinsic fluorescence of PPME through dynamic and static quenching process. The binding constants of Cu 2+ with PPME were determined at different temperatures depending on the results of fluorescence quenching. Based on the modified form of the Stern–Volmer equation, static binding constant (kS) and the dynamic binding constant (kD) of Cu 2+-PPME association were obtained at different temperatures. The static thermodynamic function of the enthalpy change (ΔHS), the dynamic thermodynamic function of the enthalpy change (ΔHD), the static thermodynamic function of the entropy change (ΔSS), and the dynamic thermodynamic function of the entropy change (ΔSD) for the binding interaction were determined according to the van't Hoff equation. The values of static Gibbs free energy change (ΔGS) and dynamic Gibbs free energy change (ΔGD) were determined to be negative indicating that the interaction process was a spontaneous. ΔHD and ΔSD values were positive indicating that the dynamic quenching process of Cu 2+-PPME interaction was driven mainly by hydrophobic forces. For the static binding quenching, ΔHS and ΔSS values were negative which indicated that hydrogen bond, electrostatic interaction, and van der Waals interaction were important driving forces for PPME- Cu 2+ association. Both static and dynamic fluorescence quenching were related to the distance between PPME and Cu 2+ indicating that the electron transfer process occurred.

Binding Properties of 2-Acetylnaphthalene with Hydroxypropyl Cyclodextrins from Fluorescence Quenching Experiments

2005 ◽  
Vol 59 (5) ◽  
pp. 691-695 ◽  
Author(s):  
Maximilian Seel ◽  
T. C. Werner
Keyword(s):  
Complex Formation ◽  
Fluorescence Quenching ◽  
Binding Site ◽  
Thermodynamic Parameters ◽  
Binding Constant ◽  
Binding Constants ◽  
Dispersion Forces ◽  
Binding Properties ◽  
Hydroxypropyl Cyclodextrins

The quenching of 2-acetylnaphthalene (2-AN) fluorescence by hydroxypropyl cyclodextrins (HP-CD) has been analyzed using modified Stern–Volmer plots to obtain binding constants as a function of temperature for 2-AN:HP-CD complexes. The HP-CDs were commercially available and contained 4–7 HP groups per CD molecule for α-CD, β-CD, and γ-CD. HP substitution causes a 12 to over 40% increase in binding constant ( Kave) for 2-AN compared to that for unsubstituted CDs, although the Kave value is not strongly dependent on the extent of HP substitution for β-CD. No evidence of formation of a 2:2 complex, such as that observed with 2-AN and γ-CD, is observed with 2-AN and HP-γ-CD. Thermodynamic parameters (ΔH°o and ΔS°o) suggest that the increase in Kave with HP substitution is due to an enlarged binding site for the HP-CDs that allows greater motional freedom for 2-AN. Comparison is made to the binding of 2-methylnaphthoate (2-MN) to CDs and HP-CDs, and the larger Kave values for 2-MN over 2-AN are attributed to greater dispersion forces for 2-MN complex formation.

scholarly journals Elucidation of Agonist and Antagonist Dynamic Binding Patterns in ER-α by Integration of Molecular Docking, Molecular Dynamics Simulations and Quantum Mechanical Calculations

2021 ◽  
Vol 22 (17) ◽  
pp. 9371
Author(s):  
Sugunadevi Sakkiah ◽  
Chandrabose Selvaraj ◽  
Wenjing Guo ◽  
Jie Liu ◽  
Weigong Ge ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Binding Site ◽  
Interaction Energy ◽  
Md Simulations ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
Dynamic Binding ◽  
Binding Interaction ◽  
Agonist And Antagonist

Estrogen receptor alpha (ERα) is a ligand-dependent transcriptional factor in the nuclear receptor superfamily. Many structures of ERα bound with agonists and antagonists have been determined. However, the dynamic binding patterns of agonists and antagonists in the binding site of ERα remains unclear. Therefore, we performed molecular docking, molecular dynamics (MD) simulations, and quantum mechanical calculations to elucidate agonist and antagonist dynamic binding patterns in ERα. 17β-estradiol (E2) and 4-hydroxytamoxifen (OHT) were docked in the ligand binding pockets of the agonist and antagonist bound ERα. The best complex conformations from molecular docking were subjected to 100 nanosecond MD simulations. Hierarchical clustering was conducted to group the structures in the trajectory from MD simulations. The representative structure from each cluster was selected to calculate the binding interaction energy value for elucidation of the dynamic binding patterns of agonists and antagonists in the binding site of ERα. The binding interaction energy analysis revealed that OHT binds ERα more tightly in the antagonist conformer, while E2 prefers the agonist conformer. The results may help identify ERα antagonists as drug candidates and facilitate risk assessment of chemicals through ER-mediated responses.

scholarly journals Evaluation of the rate constants of sugar transport through maltoporin (LamB) of Escherichia coli from the sugar-induced current noise.

1995 ◽  
Vol 105 (3) ◽  
pp. 385-401 ◽  
Author(s):  
C Andersen ◽  
M Jordy ◽  
R Benz
Keyword(s):  
Escherichia Coli ◽  
Binding Site ◽  
Outer Membrane ◽  
Rate Constants ◽  
Sugar Transport ◽  
Current Noise ◽  
Induced Current ◽  
Lipid Bilayer Membranes ◽  
Sugar Binding ◽  
Different Temperatures

LamB (maltoporin) of Escherichia coli outer membrane was reconstituted into artificial lipid bilayer membranes. The channel contains a binding site for sugars and is blocked for ions when the site is occupied by a sugar. The on and off reactions of sugar binding cause an increase of the noise of the current through the channel. The sugar-induced current noise of maltoporin was used for the evaluation of the sugar-binding kinetics for different sugars of the maltooligosaccharide series and for sucrose. The on rate constant for sugar binding was between 10(6) and 10(7) M-1.s-1 for the maltooligosaccharides and corresponds to the movement of the sugars from the aqueous phase to the central binding site. The off rate (corresponding to the release of the sugars from the channel) decreased with increasing number of glucose residues in the maltooligosaccharides from approximately 2,000 s-1 for maltotriose to 180 s-1 for maltoheptaose. The kinetics for sucrose movement was considerably slower. The activation energies of the stability constant and of the rate constants for sugar binding were evaluated from noise experiments at different temperatures. The role of LamB in the transport of maltooligosaccharides across the outer membrane is discussed.

scholarly journals The human erythrocyte anion transport protein, band 3. Characterization of exofacial alkaline titratable groups involved in anion binding/translocation.

1992 ◽  
Vol 100 (2) ◽  
pp. 301-339 ◽  
Author(s):  
P J Bjerrum
Keyword(s):  
Ionic Strength ◽  
Binding Site ◽  
Transport System ◽  
Human Erythrocyte ◽  
Binding Constant ◽  
Anion Transport ◽  
High Ionic Strength ◽  
Anion Binding ◽  
Asymmetry Factor ◽  
Sensitive Group

Chloride self-exchange across the human erythrocyte membrane at alkaline extracellular pH (pHO) and constant neutral intracellular pH (pH(i)) can be described by an exofacial deprotonatable reciprocating anion binding site model. The conversion of the transport system from the neutral to the alkaline state is related to deprotonation of a positively charged ionic strength- and substrate-sensitive group. In the absence of substrate ions ([ClO] = 0) the group has a pK of approximately 9.4 at constant high ionic strength (equivalent to approximately 150 mM KCl) and a pK of approximately 8.7 at approximately zero ionic strength. The alkaline ping-pong system (examined at constant high ionic strength) demonstrates outward recruitment of the binding sites with an asymmetry factor of approximately 0.2, as compared with the inward recruitment of the transport system at neutral pHO with an asymmetry factor of approximately 10. The intrinsic half-saturation constant for chloride binding, with [Cli] = [Clo], increased from approximately 30 mM at neutral to approximately 110 mM at alkaline pHO. The maximal transport rate was a factor of approximately 1.7 higher at alkaline pHO. This increase explains the stimulation of anion transport, the "modifier hump," observed at alkaline pHO. The translocation of anions at alkaline pHO was inhibited by deprotonation of another substrate-sensitive group with an intrinsic pK of approximately 11.3. This group together with the group with a pK of approximately 9.4 appear to form the essential part of the exofacial anion binding site. The effect of extracellular iodide inhibition on chloride transport as a function of pHO could, moreover, be simulated if three extracellular iodide binding constants were included in the model: namely, a competitive intrinsic iodide binding constant of approximately 1 mM in the neutral state, a self-inhibitor binding constant of approximately 120 mM in the neutral state, and a competitive intrinsic binding constant of approximately 38 mM in the alkaline state.

scholarly journals Substrate-Based Near-Infrared Imaging Sensors Enable Fluorescence Lifetime Contrast via Built-in Dynamic Fluorescence Quenching Elements

ACS Sensors ◽  
2016 ◽  
Vol 1 (4) ◽  
pp. 427-436 ◽  
Author(s):  
Anand T. N. Kumar ◽  
William L. Rice ◽  
Jessica C. López ◽  
Suresh Gupta ◽  
Craig J. Goergen ◽  
...  
Keyword(s):  
Fluorescence Quenching ◽  
Fluorescence Lifetime ◽  
Near Infrared ◽  
Infrared Imaging ◽  
Near Infrared Imaging ◽  
Imaging Sensors ◽  
Dynamic Fluorescence

Fluorescence quenching and the binding interaction of lumichrome with nucleic acids

2010 ◽  
Vol 55 (25) ◽  
pp. 2829-2834 ◽  
Author(s):  
Hui Li ◽  
ZhiQin Jiang ◽  
RongHua Zhang
Keyword(s):  
Fluorescence Quenching ◽  
Nucleic Acids ◽  
Binding Interaction

scholarly journals Comparative studies of the specificities of α-chymotrypsin and subtilisin BPN′. Studies with flexible and ‘locked’ substrates

1972 ◽  
Vol 126 (3) ◽  
pp. 659-665 ◽  
Author(s):  
T. N. Pattabiraman ◽  
W. B. Lawson
Keyword(s):  
Methyl Ester ◽  
Carbon Atom ◽  
Binding Site ◽  
Comparative Studies ◽  
Detrimental Effect ◽  
Optically Active ◽  
The Other ◽  
Optical Isomers ◽  
Polar Groups ◽  
Hydrolysis Of

Subtilisin BPN′ hydrolysed N-acetyl-l-3-(2-naphthyl)-alanine methyl ester, N-acetyl-l-leucine methyl ester and N-acetyl-l-valine methyl ester, faster than α-chymotrypsin. Of eight ‘locked’ substrates tested, only methyl 5,6-benzindan-2-carboxylate was hydrolysed faster by subtilisin, whereas the other esters were better substrates for chymotrypsin. Compared with the values for chymotrypsin, the stereospecific ratios during the hydrolysis of the optically active locked substrates by subtilisin were decreased by one and two orders of magnitude for bi- and tri-cyclic substrates respectively. The polar groups adjacent to the α-carbon atom of locked substrates did not contribute significantly to the reactivity of the more active optical isomers, but had a detrimental effect on the less active antipodes during hydrolysis by both the enzymes. These studies show that the binding site of subtilisin BPN′ is longer and broader than that of α-chymotrypsin.

scholarly journals The binding of cupric ions to 1-carboxymethylhistidine-119-ribonuclease

1968 ◽  
Vol 108 (4) ◽  
pp. 583-586 ◽  
Author(s):  
R. H. Saundry ◽  
W D Stein
Keyword(s):  
Binding Site ◽  
Binding Constant ◽  
Metal Ion ◽  
Binding Constants ◽  
Enzymic Activity

Binding of Cu2+ by 1-carboxymethylhistidine-119-ribonuclease was investigated by using diligand metal ion buffers. A single Cu2+-binding site was found over the Cu2+ concentration range studied. The binding constants for this site were 8·33×105 (±2%)m−1 and 1·57×104 (±6%)m−1 at pH7·0 and 6·1 respectively. An estimate of the pH-independent Cu2+-binding constant suggests that the most avid Cu2+-binding site has disappeared after carboxymethylation. This is consistent with an earlier report that binding of Cu2+ at the most avid site is associated with the loss of enzymic activity.

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