(Thio)Urea-Functionalized Cavitands as Excellent Receptors for Organic Anions in Polar Media

2004 ◽  
Vol 69 (5) ◽  
pp. 1137-1148 ◽  
Author(s):  
Gennady V. Oshovsky ◽  
Willem Verboom ◽  
David N. Reinhoudt
Keyword(s):  
Binding Sites ◽  
Binding Constants ◽  
Organic Anions ◽  
Isothermal Microcalorimetry ◽  
Polar Media

Ureidocavitand 1 and thioureidocavitand 2 bind in CH3CN organic anions such as acetate, propionate, butyrate, etc. with K values of 2-8 × 105 l mol-1 and 2-9 × 106 l mol-1, respectively, as was determined with isothermal microcalorimetry (ITC). Bringing together four (thio)urea binding sites on a molecular platform gives rise to about 2000 times higher binding constants, compared with those of the corresponding single binding sites. Glucose- and galactose-containing thioureidocavitands 5 and 6 bind acetate in 1:1 CH3CN/water with a K-value of 2.15 × 103 l mol-1.

Titration Simulations for Understanding of the Binding Equilibrium

2020 ◽  
Author(s):  
Dae Hyup Sohn
Keyword(s):  
Equilibrium Model ◽  
Binding Sites ◽  
Binding Constants ◽  
Reliability Evaluation ◽  
Binding Isotherm ◽  
Guest Chemistry

<p>The reliability evaluation of the predicted binding constants in numerous models is also a challenge for supramolecular host-guest chemistry. Here, I briefly formulate binding isotherm with the derivation of the multivalent equilibrium model for the chemist who wants to determine the binding constants of their compounds. This article gives an in-depth understanding of the stoichiometry of binding equilibrium to take divalent binding equilibria bearing two structurally identical binding sites as an example. The stoichiometry of binding equilibrium is affected by (1) the cooperativity of complex, (2) the concentration of titration media, and (3) the equivalents of guests. The simulations were conducted with simple Python codes.</p>

A comparison of cobalamin binding by liver and kidney in rat and man

1985 ◽  
Vol 68 (3) ◽  
pp. 357-364 ◽  
Author(s):  
J. S. D. Scott ◽  
E. P. W. Bowman ◽  
W. G. E. Cooksley
Keyword(s):  
Binding Sites ◽  
Plasma Membranes ◽  
Competitive Inhibition ◽  
Rat Kidney ◽  
Binding Constants ◽  
Human Kidney ◽  
Specific Adsorption ◽  
Receptor Protein ◽  
Mean Values ◽  
Liver And Kidney

1. Binding of cobalamin (Cbl) was compared in liver and kidney plasma membranes prepared from rat and human tissues. 2. Single, high-affinity, saturable (200 pmol/l), binding sites for TC II-Cbl were found in all tissues; by contrast no receptors were present for free cobalamin, for which only non-specific adsorption occurred. 3. Binding constants for TC II-CNCbl determined for liver and kidney plasma membranes were of a similar magnitude. Mean values for Ka (litre/nmol) were 16.7 (rat liver), 18.8 (rat kidney), 8.0 (human liver) and 7.5 (human kidney). 4. Results for binding TC II-OHCbl instead of TC II-CNCbl showed no difference in Ka and Bmax. values, although the non-specific adsorption was decreased to a third. 5. Competitive inhibition results showed that the receptors are specific for the TC II molecule and that binding is unaffected either by the cobalamin moiety or by the presence of free cobalamin. Degradation of the receptor protein molecules by trypsin (10 μg/ml) resulted in 90% inhibition of binding. 6. It is concluded that differences between liver and kidney in cobalamin uptake and accumulation cannot be attributed to differences in their TC II receptors.

scholarly journals Structural characterization and DNA-binding properties of Sm(III) complex with ofloxacin using spectroscopic methods

2009 ◽  
Vol 23 (2) ◽  
pp. 103-111 ◽  
Author(s):  
Changyun Chen ◽  
Kai Chen ◽  
Qi Long ◽  
Meihua Ma ◽  
Fei Ding
Keyword(s):  
Binding Sites ◽  
Nmr Spectra ◽  
Uv Spectroscopy ◽  
Binding Constants ◽  
Binding Properties ◽  
H Nmr ◽  
Elemental Analyses ◽  
Displacement Experiments ◽  
Ct Dna ◽  
Dna Binding Properties

A novel complex Sm(III) complex with ofloxacin was synthesized and characterized on the basis of elemental analyses, molar conductivities, IR spectra, thermal analysis (TG-DSC),1H-NMR spectra. Then, spectrometric titration, ethdium bromide displacement experiments by UV spectroscopy, ionic influence, viscosity measurements and Circular Dichroism (CD) spectroscopic measurements were conducted to characterize the interaction between the complex and CT-DNA. Results obtained indicate that the complex bound with CT-DNA via an intercalation mechanism. The binding constants and binding sites number of the Sm(III) complex with CT-DNA were 1.80×105l·mol−1and 1, respectively.

scholarly journals Titration Simulations for Understanding of the Binding Equilibrium

2020 ◽  
Author(s):  
Dae Hyup Sohn
Keyword(s):  
Equilibrium Model ◽  
Binding Sites ◽  
Binding Constants ◽  
Reliability Evaluation ◽  
Binding Isotherm ◽  
Guest Chemistry

<p>The reliability evaluation of the predicted binding constants in numerous models is a challenge for supramolecular host-guest chemistry. Here, I briefly formulate binding isotherm with the derivation of the multivalent equilibrium model for the chemist who wants to determine the binding constants of their compounds. This article gives an in-depth understanding of the stoichiometry of binding equilibrium to take divalent binding equilibria bearing two structurally identical binding sites as an example. The stoichiometry of binding equilibrium is affected by (1) the cooperativity of complex, (2) the concentration of titration media, and (3) the equivalents of guests. The simulations were conducted with simple Python codes.</p>

scholarly journals Free energy and kinetics of cAMP permeation through connexin26 hemichannel with and without voltage

2021 ◽  
Author(s):  
Wenjuan Jiang ◽  
Yi-Chun Lin ◽  
Wesley Botello-Smith ◽  
Jorge Contreras ◽  
Andrew L. Harris ◽  
...  
Keyword(s):  
Free Energy ◽  
Binding Sites ◽  
Binding Constants ◽  
Signaling Molecules ◽  
Potential Of Mean Force ◽  
Dynamics Simulation ◽  
Dependent Manner ◽  
Transition Rates ◽  
Molecular Signaling ◽  
Kinetics Of

AbstractThe connexin family is a diverse group of highly regulated non-β-barrel wide-pore channels permeable to biological signaling molecules. Despite their critical roles in mediating selective molecular signaling in health and disease, the molecular basis of permeation through these pores remains unclear. Here, we report the thermodynamics and kinetics of binding and transport of a second messenger, adenosine-3’,5’-cyclophosphate (cAMP), through a connexin26 hemichannel. Inward and outward fluxes of cAMP were first obtained from 4 μs simulations with voltages and multiple cAMPs in solution. The results are compared with the intrinsic potential of mean force (PMF) and the mean first passage times (MFPTs) of a single cAMP in the absence of voltage, obtained from a total of 16.5 μs of multi-replica Voronoi-tessellated Markovian milestoning simulations. The computed transit times through the pore correspond well to existing experimental data. Both voltage simulations and milestoning simulations revealed two cAMP binding sites with binding constants and dissociation rates computed from PMF and MFPTs. The protein dipole inside the pore produces an asymmetric PMF, reflected in unequal cAMP MFPTs in each direction once within the pore. The free energy profiles under voltages derived from intrinsic PMF provided a unified understanding of directional transition rates with/without voltage, and revealed the unique role of channel polarity and the mobile electrolyte within a wide pore on the total free energy. In addition, we show how these factors influence the cAMP dipole vector during permeation, and how cAMP affects the local and non-local pore diameter in a position-dependent manner.Significance StatementConnexins are wide-pore channels permeable to cellular signaling molecules. They mediate molecular signaling crucial in physiology, pathology, and development; mutations in connexins cause human pathologies. However, the fundamental structural, thermodynamic, and kinetic determinants of molecular permeability properties are unknown. Using multiple molecular dynamics simulation techniques, we report, for the first time, an in-depth investigation of the free energy and the directional transition rates of an important biological signaling molecule, cAMP, through a connexin channel. We reveal the energetics and binding sites that determine the cAMP flux, and the effects of mobile ions and external electrical field on the process. The results provide a basis for understanding the unique features of molecular flux through connexins and other non-β-barrel wide-pore channels.

Graphical determination of specific activity, binding constants, and antibody-site concentrations for radioimmunoassays, with application to thymopoietin.

1980 ◽  
Vol 26 (6) ◽  
pp. 718-723
Author(s):  
F H Verhoff ◽  
P J Lisi ◽  
C D Fischer ◽  
J W Teipel ◽  
G Goldstein ◽  
...  
Keyword(s):  
Binding Sites ◽  
Specific Activity ◽  
Binding Constants ◽  
Experimental Information ◽  
Antibody Binding ◽  
Displacement Analysis ◽  
Additional Information ◽  
Graphical Technique ◽  
Materials Used

Abstract A graphical procedure for determining the specific activity of radiolabeled ligands has been developed for use with radioimmunoassays. Although with this procedure we utilize the same experimental information required for displacement analysis, we are also able to determine both the specific activity and the binding constants of the labeled and unlabeled materials without assuming that these constants are equal; the concentration of antibody-binding sites can also be calculated. Thus, this graphical technique permits calculation of additional information without additional experimentation. We applied this procedure to the labeled materials used in a thymopoietin assay, testing two different preparations of radiolabeled material, and saw negligible differences between the two. The specific activity determined from the displacement analysis correlated well with that calculated by the graphical procedure.

scholarly journals Interaction Between α-Glucosidase Inhibitor with Common Blood Proteins: A Thermodynamic and Spectroscopic Studies

2020 ◽  
Vol 32 (7) ◽  
pp. 1756-1762
Author(s):  
K.M. Sachin ◽  
Sameer A. Karpe ◽  
Man Singh ◽  
Ajaya Bhattarai
Keyword(s):  
Circular Dichroism ◽  
Serum Albumin ◽  
Binding Sites ◽  
Binding Constants ◽  
Spectroscopic Studies ◽  
Blood Proteins ◽  
Glucosidase Inhibitors ◽  
Number Of Binding Sites ◽  
Treatment Of Diabetes ◽  
Circular Dichroïsm

The interaction of an α-glucosidase inhibitors class of drug acarbose with globular proteins like bovine serum albumin (BSA), human serum albumin (HSA) and haemoglobin studied by fluorescence, circular dichroism (CD) spectroscopic methods. Acarbose is used for the treatment of diabetes mellitus type 2 and in some countries, prediabetes. The quenching constant (kq) values were calculated by using fluorescence data, higher with haemoglobin (at λext = 405 nm). It indicates the quenching process for the acarbose-haemoglobin interaction. Thus, the binding constants (kb), infers that the electrostatic, hydrogen bonding, and intermolecular interactions play an important role in the proteins, and drug interaction. The number of binding sites (n), between BSA, HSA and haemoglobin with acarbose was estimated by fluorescence data, the highest binding sites (15.55) of acarbose-haemoglobin at (λext = 405nm) indicates that the strong interaction or high quenching interaction. The interactions between BSA, HSA and haemoglobin with acarbose were confirmed by spectroscopic analysis and thermodynamic determination. The circular dichroism (CD) spectra implied the significant change in the conformation of BSA, HSA and haemoglobin upon binding with acarbose.

Temperature Dependent Conformation Changes of Ribulose-1,5-bisphosphate Carboxylase Studied by the Use of 1-Anilino-8-naphthalene Sulfonate

1977 ◽  
Vol 32 (3-4) ◽  
pp. 226-228 ◽  
Author(s):  
Günter F. Wildner ◽  
Jürgen Henkel
Keyword(s):  
Enzyme Activity ◽  
Binding Sites ◽  
Fluorescence Probe ◽  
Fluorescence Emission ◽  
Binding Constants ◽  
Temperature Dependent ◽  
Bisphosphate Carboxylase ◽  
Influence Of Temperature On ◽  
Number Of Binding Sites ◽  
Enzyme Molecules

Abstract The influence of temperature on the structure and enzyme activity of ribulose-1,5-bisphosphate carboxylase, isolated from Euglena gracilis cells, was studied. Freezing of the purified ribulose-1,5-bisphosphate carboxylase preparation causes a severe loss of enzyme activity, which can be restored again by incubation of the enzyme molecules at higher temperatures (50 °C). The titration of both enzyme samples with the fluorescence probe 1-anilino-8-naphthalene sulfonate (ANS) re­vealed an increase of the fluorescence emission of the low temperature form of the enzyme. Two different enzyme conformations can be assumed which differ in the number of binding sites for ANS and Vmax values for the carboxylase reaction but show similar binding constants for ANS and the apparent Km values for C02 .

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