Does the ligand-biopolymer equilibrium binding constant depend on the number of bound ligands?

Biopolymers ◽  
2010 ◽  
Vol 93 (11) ◽  
pp. 932-935 ◽  
Author(s):  
Daria A. Beshnova ◽  
Anastasia O. Lantushenko ◽  
Maxim P. Evstigneev
Keyword(s):  
Binding Constant ◽  
Equilibrium Binding ◽  
Equilibrium Binding Constant

scholarly journals The linkage between binding of the C-terminal domain of hirudin and amidase activity in human α-thrombin

1993 ◽  
Vol 289 (2) ◽  
pp. 475-480 ◽  
Author(s):  
R de Cristofaro ◽  
B Rocca ◽  
B Bizzi ◽  
R Landolfi
Keyword(s):  
Rate Constants ◽  
Binding Constant ◽  
Amidase Activity ◽  
Equilibrium Binding ◽  
Viscosity Effects ◽  
The Individual ◽  
Individual Rate ◽  
Hydrolysis Of ◽  
Equilibrium Binding Constant

A method derived from the analysis of viscosity effects on the hydrolysis of the amide substrates D-phenylalanylpipecolyl-arginine-p-nitroaniline, tosylglycylprolylarginine-p-nitroanaline and cyclohexylglycylalanylarginine-p-nitroalanine by human alpha-thrombin was developed to dissect the Michaelis-Menten parameters Km and kcat into the individual rate constants of the binding, acylation and deacylation reactions. This method was used to analyse the effect of the C-terminal hirudin (residues 54-65) [hir-(54-65)] domain on the binding and hydrolysis of the three substrates. The results showed that the C-terminal hir-(54-65) fragment affects only the acylation rate, which is increased approx. 1.2-fold for all the substrates. Analysis of the dependence of acylation rate constants on hirudin-fragment concentration, allowed the determination of the equilibrium binding constant of C-terminal hir-(54-65) (Kd approximately 0.7 microM). In addition this peptide was found to competitively inhibit thrombin-fibrinogen interaction with a Ki which is in excellent agreement with the equilibrium constant derived from viscosity experiments. These results demonstrate that binding of hir-(54-65) to the fibrinogen recognition site of thrombin does not affect the equilibrium binding of amide substrates, but induces only a small increase in the acylation rate of the hydrolysis reaction.

scholarly journals A comparison of acylation, phosphorylation and binding in related substrates and inhibitors of serum cholinesterase

1966 ◽  
Vol 101 (3) ◽  
pp. 584-590 ◽  
Author(s):  
A R Main ◽  
F L Hastings
Keyword(s):  
Rate Constant ◽  
Binding Constant ◽  
Binding Energies ◽  
Serum Cholinesterase ◽  
P Values ◽  
Ethyl Methyl ◽  
Equilibrium Binding ◽  
Alkyl Groups ◽  
Inhibition Constants ◽  
Equilibrium Binding Constant

1. The K(m) and catalytic-centre activities for human serum cholinesterase and methyl, ethyl, n-propyl and n-butyl butyrate substrates were determined and compared with the related inhibition constants of a similarly substituted organophosphate inhibitor series based on malaoxon. The results indicated that the catalytic-centre activities approximated to k(+2(a)), the acylation rate constant, and that K(m) approximated to the equilibrium binding constant. The inhibition constants measured were K(a), the equilibrium binding constant, and k(+2(p)), the phosphorylation rate constant. 2. The effects of the alkyl substituents on k(+2(p)) and k(+2(a)) were closely parallel, and the decreasing order in each case was: n-butyl; methyl; n-propyl; ethyl. The Taft constants did not follow this order, suggesting that alkyl substituents did not primarily effect acylation or phosphorylation by electron induction. 3. For comparable homologues, the k(+2(a)) values were on average 435 times the k(+2(p)) values. The k(+2(p)) values at 25 degrees and pH7.6 ranged from 6.6min.(-1) for the diethyl member to 22.6min.(-1) for the di-n-butyl member. 4. The effect of the alkyl substituents on K(a) and K(m) were closely paralleled. The increasing order in each case was: n-butyl; n-propyl; ethyl; methyl. The K(a) values were about 100 times less than the comparable K(m) values. 5. Consideration of the binding energies suggested that only one of the two alkyl groups on the malaoxon homologues bound to the active site. 6. The possibility that malaoxon acted as a substrate as well as an inhibitor for cholinesterase was also investigated, but no evidence of a substrate reaction was found.

scholarly journals Photochemical and ligand-exchange properties of the cyanide complex of fully reduced cytochrome c oxidase

1991 ◽  
Vol 279 (2) ◽  
pp. 355-360 ◽  
Author(s):  
B C Hill ◽  
S Marmor
Keyword(s):  
Binding Site ◽  
Cytochrome Oxidase ◽  
Ligand Exchange ◽  
Binding Constant ◽  
First Order ◽  
Structure And Dynamics ◽  
Equilibrium Binding ◽  
Recombination Kinetics ◽  
Equilibrium Binding Constant ◽  
Reduced State

Cytochrome oxidase, in its fully reduced state, forms a complex with CN having a Kd of 230 microM with a stoicheiometry of 1 CN molecule per cytochrome oxidase. We do not detect a second CN-binding site as seen by i.r. spectroscopy [Yoshikawa & Caughey (1990) J. Biol. Chem. 265, 7945-7958]. The ferrocytochrome a3-CN complex, like the analogous ferrocytochrome a3-CO complex, is photosensitive but with a 15-fold lower quantum yield for photolysis. Analysis of the recombination kinetics after CN photolysis establishes a simple bimolecular binding constant of 235 M-1.s-1, in agreement with the value obtained from stopped-flow studies [Antonini, Brunori, Greenwood, Malmström & Rotillo (1971) Eur. J. Biochem. 23, 396-400]. A rate of 0.07 s-1 for the first-order dissociation of CN from cytochrome a3 is found by the rate of exchange of CO with ferrocytochrome a3-CN, and is consistent with the value calculated from the equilibrium binding constant and the CN on rate. However, O2 is able to oxidize the fully reduced CN compound at a rate well in excess of the CN off rate. The product of this oxidation reaction is a partially reduced CN complex. This implies that O2 either promotes CN dissociation or is able to oxidize the CN-bound enzyme directly. These results are discussed in the context of the structure and dynamics of the ligand-binding site of cytochrome oxidase.

scholarly journals Applying support-vector machine learning algorithms toward predicting host–guest interactions with cucurbit[7]uril

2020 ◽  
Vol 22 (26) ◽  
pp. 14976-14982
Author(s):  
Anthony Tabet ◽  
Thomas Gebhart ◽  
Guanglu Wu ◽  
Charlie Readman ◽  
Merrick Pierson Smela ◽  
...  
Keyword(s):  
Machine Learning ◽  
Support Vector Machine ◽  
Support Vector Machines ◽  
Small Molecules ◽  
Binding Constant ◽  
Machine Learning Algorithms ◽  
Support Vector ◽  
Equilibrium Binding ◽  
Vector Machines ◽  
Equilibrium Binding Constant

We evaluate the ability of support-vector machines to predict the equilibrium binding constant of small molecules to cucurbit[7]uril.

scholarly journals pH-dependence and structure–activity relationships in the papain-catalysed hydrolysis of anilides

1971 ◽  
Vol 124 (1) ◽  
pp. 117-122 ◽  
Author(s):  
G. Lowe ◽  
Y. Yuthavong
Keyword(s):  
Acid Catalysis ◽  
Ph Dependence ◽  
Base Catalysis ◽  
General Base ◽  
Structure Activity ◽  
Equilibrium Binding ◽  
General Acid ◽  
Leaving Group ◽  
Hydrolysis Of ◽  
Equilibrium Binding Constant

The pH-dependence of the Michaelis–Menten parameters for the papain-catalysed hydrolysis of N-acetyl-l-phenylalanylglycine p-nitroanilide was determined. The equilibrium binding constant, Ks, is independent of pH between 3.7 and 9.3, whereas the acylation constant, k+2, shows bell-shaped pH-dependence with apparent pKa values of 4.2 and 8.2. The effect of substituents in the leaving group on the acylation constant of the papain-catalysed hydrolysis of hippuryl anilides and N-acetyl-l-phenylalanylglycine anilides gives rise in both series to a Hammett ρ value of -1.04. This indicates that the enzyme provides electrophilic, probably general-acid, catalysis, as well as the nucleophilic or general-base catalysis previously found. A mechanism involving a tetrahedral intermediate whose formation is general-base-catalysed and whose breakdown is general-acid-catalysed seems most likely. The similarity of the Hammett ρ values appears to exclude facilitated proton transfer as a means through which the specificity of papain is expressed.

scholarly journals Presence of sterol-binding sites in the cytosol of French-bean (Phaseolus vulgaris) roots

1988 ◽  
Vol 250 (2) ◽  
pp. 565-569 ◽  
Author(s):  
M A Vega ◽  
R L Boland
Keyword(s):  
Phaseolus Vulgaris ◽  
Vitamin D3 ◽  
Binding Sites ◽  
Specific Binding ◽  
French Bean ◽  
Binding Reaction ◽  
Equilibrium Binding ◽  
Tissue Responses ◽  
Equilibrium Binding Constant ◽  
Sterol Binding

Vitamin D3 (cholecalciferol) and stigmasterol have been shown to stimulate Ca2+ uptake and to induce calmodulin synthesis in cultured French-bean (Phaseolus vulgaris) roots. In addition, the appearance of calmodulin in the cultures in response to vitamin D3 could be prevented by RNA-synthesis inhibitors. To investigate the possibility that the sterols affect root DNA transcription through a receptor-mediated mechanism, the existence of sterol-binding sites in P. vulgaris roots was investigated. Specific binding of [3H]vitamin D3 could be demonstrated with intact tissue and the cytosolic fraction obtained therefrom. Equilibrium in the binding reaction with cytosol was attained after 4 h of incubation at 0 degrees C. The [3H]vitamin D3 was reversibly bound, since it could be displaced by an excess of unlabelled sterol. An equilibrium binding constant (KD) of (3.48 +/- 0.09) x 10(-9) M and a maximum binding-site concentration (nmax) of 32 +/- 2.54 (3) pmol/mg of protein could be calculated by Scatchard [(1949) Ann. N.Y. Acad. Sci. 51, 660-672] analysis. In addition to vitamin D3, stigmasterol and sitosterol were effectively able to compete with [3H]vitamin D3 for binding to root cytosol. Cortisol, oestradiol and progesterone displaced bound labelled vitamin D3 to a lesser extent, whereas 5 beta-dihydrotestosterone, lanosterol and diosgenin were ineffective. The affinity and specificity of the root sterol-binding sites are in agreement with the characteristics of tissue responses to the sterols (Ca2+ uptake and calmodulin synthesis).

scholarly journals Resolution of the Equilibrium Constant for the T State → RState Conformational Change of Human Hemoglobin into Endothermic and Exothermic Component Reactions

2019 ◽  
Author(s):  
Francis Knowles ◽  
Douglas Magde
Keyword(s):  
Equilibrium Constant ◽  
Whole Blood ◽  
Binding Constant ◽  
Binary Complex ◽  
Human Hemoglobin ◽  
Conformation Change ◽  
Unknown Quantity ◽  
Equilibrium Binding ◽  
Binding Data ◽  
T State

<p> The dimensionless equilibrium constant for the allosteric conformation change, K<sub>ΔC</sub> = 0.02602 (Knowles & Magde, linked ms 2) following binding of O<sub>2</sub> by α-chains in <sup>T</sup>state Hb<sub>4</sub>/BPG (whole blood under standard conditions) is shown to be comprised of: (i) an endothermic change in conformation, from <sup>T</sup>state to <sup>R</sup>state, of 24.3 kJ/mol; (ii) exothermic conversion of <sup>T</sup>state <sup>T</sup>αO<sub>2</sub>-chains to <sup>R</sup>state <sup>R</sup>αO<sub>2</sub>-chains of -13.8 kJ/mol; (iii)exothermic binding of BPG by R-states. Eq. (1) defines the component steps whereby the <sup>T</sup>state conformation is converted to the <sup>R</sup>state conformation.</p> <p>ΔG<sup>o</sup>(<sup>R</sup>(Hb<sub>4</sub>), BPG) describes the endothermic decomposition of the binary complex, <sup>T</sup>Hb<sub>4</sub>/BPG into <sup>R</sup>Hb<sub>4</sub> and BPG, equal to + 33.7 kJ/mol (DeBruin et al. (1973). J. Biol. Chem. <u>248</u>, 2774-2777). ΔG<sup>o</sup> for the equilibrium constant for ΔG<sup>O</sup>(K<sub>ΔC</sub>) and Σ ΔG<sup>o</sup> for binding of O<sub>2</sub> by the pair of equivalent <sup>T</sup>state α-chains, ΔG<sup>O</sup>(<sup>T</sup>α<sup>*</sup>O<sub>2</sub>), + 9.41 kJ/mol and – 49.6 kJ/mol, respectively, are determined by fitting of O<sub>2</sub> equilibrium binding data to the Perutz-Adair equation. ΔG<sup>o</sup> for reaction of a pair of equivalent <sup>R</sup>state α-chains with O<sub>2</sub>, ΔG<sup>O</sup>(<sup>R</sup>αO<sub>2</sub>), was estimated from the known affinity of myoglobin for O<sub>2</sub> at 37<sup>o</sup>C (Theorell H. (1936). Biochem. Z., <u>268</u>, 73-81), -63.4 kJ/mol. The unknown quantity, ∆G<sup>O</sup>(<sup>R</sup>(HbO<sub>2</sub>)<sub>4</sub>/BPG), was obtained by solving Eq. (1), being -10.5 kJ/mol, K (<sup>R</sup>(HbO<sub>2</sub>)<sub>4</sub>/BPG) = 58.4 L/mol. The value of the equilibrium constant for binding BPG to R-state conformations represents 0.0073% of the value of the binding constant of BPG to <sup>T</sup>state conformations: 800,000 L/mol. The value of K<sub>ΔC</sub>; (i) accounts for the ability of O<sub>2</sub> to escape, virtually unhindered from rbcs and (ii) provides a biophysical basis for manifestation of high resting rates of metabolism in warm blooded species.</p>

Thermal Management Design of a Nanoscale Biocalorimeter

2007 ◽  
Author(s):  
Gregory J. Kowalski ◽  
Amir Talakoub ◽  
Dale Larson
Keyword(s):  
Surface Plasmon ◽  
Index Of Refraction ◽  
Significant Advance ◽  
Biochemical Reactions ◽  
Nanohole Array ◽  
Temperature Changes ◽  
Equilibrium Binding ◽  
Concentration Changes ◽  
Induced Changes ◽  
Equilibrium Binding Constant

A nanoscale calorimeter design based on temperature induced changes in a surface plasmon based photonics effect has the potential to decrease the mass of experimental compounds consumed and to increase the throughput of experiments investigating drug development. This calorimeter is based on a demonstrated surface plasmon biosensor in which index of refraction changes as small as 10−5 % caused by biochemical reactions on the sensor surface are detected. To achieve this sensitivity require that the device’s temperature be held constant to within ± 0.001 K. In the biosensor the temperature was held constant to measure the concentration changes. For the calorimeter the concentration is held constant and temperature changes are monitored. In the calorimeter design the nanohole array sensor will be used as a sensitive thermometer that will be used to determine the enthalpy of binding, equilibrium binding constant and entropy changes of biochemical reactions. The numerical analysis described in this work demonstrates that nanoscale calorimetry is possible. The simulations demonstrate that two designs can produce temperature rises of 5.5 and 40 C, respectively well above the (10−3) C resolution of the sensors. These results were obtained using less than three orders of magnitude less reactants than is currently being used in calorimetry studies which is a significant advance of this technology.

Imprinted CS Membrane Using EGCG as Template

2012 ◽  
Vol 512-515 ◽  
pp. 1630-1633
Author(s):  
Sheng Chen ◽  
Hua Xiu Lan ◽  
Xiu Ling Ma
Keyword(s):  
Aqueous Media ◽  
Scatchard Analysis ◽  
Functional Monomer ◽  
Excellent Performance ◽  
Molecularly Imprinted ◽  
Equilibrium Binding ◽  
Before And After ◽  
Molecularly Imprinted Membrane ◽  
Equilibrium Binding Constant ◽  
Imprinted Membrane

A molecularly imprinted membrane was prepared in aqueous media using CS as functional monomer, EGCG as template molecules. The morphologies of molecularly imprinted membrane before and after modification with porogen (PEG) were observed by SEM. The imprinted membrane showed an excellent performance after several times adsorption and desorption. According to Scatchard analysis, the result showed that the imprinted membrane had a binding site for EGCG, the max adsorption capacity of imprinted membrane and equilibrium binding constant arrived at 49.52 mg/g, 4.046, respectively

Sign in / Sign up

Export Citation Format

Share Document