scholarly journals pH-dependence of warfarin binding to α1-acid glycoprotein (orosomucoid)

1993 ◽  
Vol 289 (3) ◽  
pp. 767-770 ◽  
Author(s):  
S Urien ◽  
F Brée ◽  
B Testa ◽  
J P Tillement
Keyword(s):  
Hydrogen Bond ◽  
Binding Site ◽  
Ph Dependence ◽  
Protonated Form ◽  
Association Constants ◽  
Histidine Residue ◽  
Difference Spectra ◽  
Acid Glycoprotein ◽  
Binding Data ◽  
Decreasing Ph

The binding of warfarin to alpha 1-acid glycoprotein (AAG) was found to increase with decreasing pH. The u.v.-visible difference spectra generated upon binding to AAG at pH 5.0 or 7.4 showed warfarin to bind as the anion. Warfarin-binding data were satisfactorily fitted to a model that incorporates the effect of pH and discriminates the association constants of the non-protonated and protonated binding site of the protein. It was shown that AAG-binding site in the protonated form had a markedly higher affinity for warfarin than the non-protonated form, with a pK value of 7.7 +/- 0.1, which is likely to be a histidine residue. Among other possible interactions, it is suggested that ligand binding to AAG involves a reinforced hydrogen bond.

scholarly journals pH-dependency of basic ligand binding to α1-acid glycoprotein (orosomucoid)

1991 ◽  
Vol 280 (1) ◽  
pp. 277-280 ◽  
Author(s):  
S Urien ◽  
F Brée ◽  
B Testa ◽  
J P Tillement
Keyword(s):  
Hydrophobic Interactions ◽  
Association Constants ◽  
Affinity Binding ◽  
Neutral Form ◽  
Difference Spectra ◽  
Acid Glycoprotein ◽  
High Affinity ◽  
Ph Dependency ◽  
Binding Data ◽  
Protonated Forms

The binding interactions of a series of basic ligands with alpha 1-acid glycoprotein (AAG) were examined as a function of pH. The binding to AAG increased with increasing pH, and the binding data were satisfactorily fitted to a model that incorporates the effect of pH and discriminates the association constants of neutral (non-protonated) and protonated forms of ligands. It was shown that ligands in the neutral form have a markedly higher affinity for AAG than the protonated forms, resulting in a concomitant decrease in the pKa of bound ligands. The u.v.-visible difference spectra generated upon binding of a representative ligand to AAG also showed that there was a contribution to the binding arising from the deprotonation of the ligand. It is suggested that all tested ligands bind similarly to AAG and that hydrophobic interactions dominate high-affinity binding to AAG.

scholarly journals Interactions between inhibitors of dihydrofolate reductase

1989 ◽  
Vol 258 (2) ◽  
pp. 335-342 ◽  
Author(s):  
K Bowden ◽  
A D Hall ◽  
B Birdsall ◽  
J Feeney ◽  
G C K Roberts
Keyword(s):  
Steady State ◽  
Binding Site ◽  
Dihydrofolate Reductase ◽  
Binding Sites ◽  
High Field ◽  
Ph Dependence ◽  
Histidine Residue ◽  
Adenine Ring ◽  
Steady State Kinetics ◽  
Pka Value

The binding of substrates and inhibitors to dihydrofolate reductase was studied by steady-state kinetics and high-field 1H-n.m.r. spectroscopy. A series of 5-substituted 2,4-diaminopyrimidines were examined and were found to be ‘tightly binding’ inhibitors of the enzyme (Ki less than 10(-9) M). Studies on the binding of 4-substituted benzenesulphonamides and benzenesulphonic acids also established the existence of a ‘sulphonamide-binding site’ on the enzyme. Subsequent n.m.r. experiments showed that there are two binding sites for the sulphonamides on the enzyme, one of which overlaps the coenzyme (NADPH) adenine-ring-binding site. An examination of the pH-dependence of the binding of sulphonamides to the enzyme indicated the influence of an ionizable group on the enzyme that was not directly involved in the sulphonamide binding. The change in pKa value from 6.7 to 7.2 observed on sulphonamide binding suggests the involvement of a histidine residue, which could be histidine-28.

scholarly journals Diethyl pyrocarbonate modification of the ryanodine receptor/Ca2+ channel from skeletal muscle

1994 ◽  
Vol 299 (1) ◽  
pp. 177-181 ◽  
Author(s):  
V Shoshan-Barmatz ◽  
S Weil
Keyword(s):  
Binding Site ◽  
Ryanodine Receptor ◽  
Time Course ◽  
Ph Dependence ◽  
Histidine Residue ◽  
Binding Affinities ◽  
Single Class ◽  
Diethyl Pyrocarbonate ◽  
Dependent Inactivation ◽  
Specific Reagent

Exposure of junctional sarcoplasmic reticulum (SR) membranes or purified ryanodine receptor to the histidine-specific reagent diethyl pyrocarbonate (DEPC) led to concentration- and time-dependent inactivation of ryanodine binding. The pH-dependence of the inactivation of ryanodine binding by DEPC and the reversal of this inactivation by hydroxylamine suggests the modification of histidine residue(s) by the reagent. Kinetic analysis of the time course of inactivation of ryanodine binding by DEPC suggests that the inactivation resulted from modification of a single class of histidine residue per ryanodine-binding site. The degree of inactivation of ryanodine binding by DEPC was decreased when high NaCl concentrations were present in the modification medium. The binding affinities for ryanodine and Ca2+ were not altered by DEPC modification. This modification decreased the total ryanodine-binding sites. DEPC modification increased the Ca(2+)-permeability of the SR vesicles. A variety of bivalent cations prevented the DEPC inactivation of ryanodine binding in a series of decreasing efficiency: Mn2+ > Ba2+ > Mg2+ > Ca2+, similar to their effectiveness in inhibiting ryanodine binding. It is suggested that a histidine residue(s) in the ryanodine receptor is involved, either in the binding of Ca2+, or in a conformational change that may be required for Ca2+ binding to its binding site(s). This modification of the ryanodine receptor resulted in inactivation of ryanodine binding and activation of Ca2+ release.

scholarly journals Functional characterization of the dimerization domain of the ferric uptake regulator (Fur) of Pseudomonas aeruginosa

2006 ◽  
Vol 400 (3) ◽  
pp. 385-392 ◽  
Author(s):  
Erdeni Bai ◽  
Federico I. Rosell ◽  
Bao Lige ◽  
Marcia R. Mauk ◽  
Barbara Lelj-Garolla ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Metal Ions ◽  
Binding Site ◽  
Metal Ion ◽  
Association Constants ◽  
Ion Binding ◽  
Ferric Uptake Regulator ◽  
Metal Ion Binding ◽  
Dimerization Domain ◽  
High Affinity

The functional properties of the recombinant C-terminal dimerization domain of the Pseudomonas aeruginosa Fur (ferric uptake regulator) protein expressed in and purified from Escherichia coli have been evaluated. Sedimentation velocity measurements demonstrate that this domain is dimeric, and the UV CD spectrum is consistent with a secondary structure similar to that observed for the corresponding region of the crystallographically characterized wild-type protein. The thermal stability of the domain as determined by CD spectroscopy decreases significantly as pH is increased and increases significantly as metal ions are added. Potentiometric titrations (pH 6.5) establish that the domain possesses a high-affinity and a low-affinity binding site for metal ions. The high-affinity (sensory) binding site demonstrates association constants (KA) of 10(±7)×106, 5.7(±3)×106, 2.0(±2)×106 and 2.0(±3)×104 M−1 for Ni2+, Zn2+, Co2+ and Mn2+ respectively, while the low-affinity (structural) site exhibits association constants of 1.3(±2)×106, 3.2(±2)×104, 1.76(±1)×105 and 1.5(±2)×103 M−1 respectively for the same metal ions (pH 6.5, 300 mM NaCl, 25 °C). The stability of metal ion binding to the sensory site follows the Irving–Williams order, while metal ion binding to the partial sensory site present in the domain does not. Fluorescence experiments indicate that the quenching resulting from binding of Co2+ is reversed by subsequent titration with Zn2+. We conclude that the domain is a reasonable model for many properties of the full-length protein and is amenable to some analyses that the limited solubility of the full-length protein prevents.

Iron-Blocking the High-Affinity Mn-Binding Site in Photosystem II Facilitates Identification of the Type of Hydrogen Bond Participating in Proton-Coupled Electron Transport via YZ•†

Biochemistry ◽  
2005 ◽  
Vol 44 (28) ◽  
pp. 9746-9757 ◽  
Author(s):  
Boris K. Semin ◽  
Elena R. Lovyagina ◽  
Kirill N. Timofeev ◽  
Ilya I. Ivanov ◽  
Andrei B. Rubin ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Electron Transport ◽  
Photosystem Ii ◽  
Binding Site ◽  
High Affinity

scholarly journals Single Molecule Investigation of Ag+ Interactions with Single Cytosine-, Methylcytosine- and Hydroxymethylcytosine-Cytosine Mismatches in a Nanopore

2014 ◽  
Vol 4 (1) ◽  
Author(s):  
Yong Wang ◽  
Bin-Quan Luan ◽  
Zhiyu Yang ◽  
Xinyue Zhang ◽  
Brandon Ritzo ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Binding Site ◽  
Single Molecule ◽  
Metal Ion ◽  
Detection Method ◽  
Direct Detection ◽  
Alpha Hemolysin ◽  
Duplex Stability ◽  
Dynamics Simulations ◽  
Direct Detection Method

Abstract Both cytosine-Ag-cytosine interactions and cytosine modifications in a DNA duplex have attracted great interest for research. Cytosine (C) modifications such as methylcytosine (mC) and hydroxymethylcytosine (hmC) are associated with tumorigenesis. However, a method for directly discriminating C, mC and hmC bases without labeling, modification and amplification is still missing. Additionally, the nature of coordination of Ag+ with cytosine-cytosine (C-C) mismatches is not clearly understood. Utilizing the alpha-hemolysin nanopore, we show that in the presence of Ag+, duplex stability is most increased for the cytosine-cytosine (C-C) pair, followed by the cytosine-methylcytosine (C-mC) pair and the cytosine-hydroxymethylcytosine (C-hmC) pair, which has no observable Ag+ induced stabilization. Molecular dynamics simulations reveal that the hydrogen-bond-mediated paring of a C-C mismatch results in a binding site for Ag+. Cytosine modifications (such as mC and hmC) disrupted the hydrogen bond, resulting in disruption of the Ag+ binding site. Our experimental method provides a novel platform to study the metal ion-DNA interactions and could also serve as a direct detection method for nucleobase modifications.

Effect of the hydrogen bond network in carbonic anhydrase II zinc binding site. A theoretical study

1998 ◽  
Vol 76 (7) ◽  
pp. 1027-1032 ◽  
Author(s):  
Silvia Álvarez-Santos ◽  
Àngels González-Lafont ◽  
José M Lluch
Keyword(s):  
Hydrogen Bond ◽  
Carbonic Anhydrase ◽  
Binding Site ◽  
Zinc Binding ◽  
Carbonic Anhydrase Ii ◽  
Am1 Method ◽  
Hydrogen Bond Network ◽  
Zinc Binding Site ◽  
Bond Network ◽  
Metal Ligand

The hydrogen bond network influence on the carbonic anhydrase II (CAII) zinc binding site has been studied theoretically by using the semiempirical AM1 method. To this aim, quantum mechanical reduced models of wild-type CAII and several CAII variants have been constructed. We have shown that, when a direct metal ligand donates a hydrogen bond to an indirect metal ligand, the first-shell residues enhance their electrostatic interaction with the zinc cation. Thus, the hydrogen-bond network is able to modulate the zinc binding affinity and the zinc-water pKa.Key words: hydrogen bond network, carbonic anhydrase II, Zn2+ metalloenzyme ligands.

scholarly journals The pKa of the catalytic histidine residue of chloramphenicol acetyltransferase

1993 ◽  
Vol 290 (1) ◽  
pp. 15-19 ◽  
Author(s):  
A Lewendon ◽  
W V Shaw
Keyword(s):  
Chemical Modification ◽  
Ph Dependence ◽  
Thiol Group ◽  
Chloramphenicol Acetyltransferase ◽  
Histidine Residue ◽  
Pka Values ◽  
Primary Hydroxy Group ◽  
Pka Value ◽  
Catalytic Role ◽  
Kinetics Of

A catalytically essential histidine residue (His-195) of chloramphenicol acetyltransferase (CAT) acts as a general base in catalysis, abstracting a proton from the primary hydroxy group of chloramphenicol. The pKa of His-195 has been determined from the pH-dependence of chemical modification. Both methyl 4-nitrobenzenesulphonate and iodoacetamide inactivate CAT by irreversible modification of His-195. The kinetics of inactivation by methyl 4-nitrobenzenesulphonate are pseudo-first-order, and the pH-dependence of inactivation yields a pKa value of 6.60. Iodoacetamide inactivation proceeds with second-order kinetics and a pKa value of 6.80. An alternative site of modification at the active site of CAT is the thiol group of Cys-31, a residue which has no catalytic role. On replacement of Cys-31 with alanine (Ala-31 CAT), the pH-dependence of iodoacetamide inactivation gives a pKa value of 6.66. The pKa values derived from chemical-modification experiments directed at His-195 are in agreement with the pKa values of 6.62 and 6.61 determined for wild-type and Ala-31 CAT respectively from the pH-dependence of kcat/Km.

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